Langmuir-Blodgett Films As Models for Tof

The Pennsylvania State University

The Graduate School

Department of Chemistry

LANGMUIR-BLODGETT FILMS AS MODELS FOR TOF-

SIMS INVESTIGATION OF BIOLOGICAL SYSTEMS

A Dissertation in

Chemistry

Leiliang Zheng

Submitted in Partial Fulfillment of the Requirements for the Degree of

Doctor of Philosophy

August 2008

The dissertation of Leiliang Zheng was reviewed and approved* by the following:

Nicholas Winograd Evan Pugh Professor of Chemistry Dissertation Advisor Chair of Committee

Barbara Garrison Shapiro Professor of Chemistry

Christine D. Keating Associate Professor of Chemistry

Ahmed A. Heikal Associate Professor of Bioengineering

Ayusman Sen Professor of Chemistry Head of the Department of Chemistry

*Signatures are on file in the Graduate School

iii ABSTRACT

The work presented in this thesis is aimed at utilizing Langmuir-Blodgett (LB) films as model biological systems to improve fundamental understandings and expand applications of time-of-flight secondary ion mass spectrometry (TOF-SIMS) bioanalysis.

Chemical imaging of ternary lipid LB monolayer systems shows that it is possible to study lipid-lipid interactions by TOF-SIMS. The incorporation of membrane proteins into the lipid LB monolayer leads to a more representative model and TOF-SIMS imaging is able to identify the membrane protein in the model membrane. Chemically alternating LB multilayer films are developed as a model for fundamental investigations of molecular depth profiling. Organic-organic interface widths are quantitatively studies as a function of temperature, surface topography, and primary ion energy and incident angle. Three-dimensional imaging of the alternating multilayer films visibly displays the

“crater effect” and the effect of data acquisition range on interface width measurement is quantitatively studied.

iv TABLE OF CONTENTS

LIST OF FIGURES ...... vii

LIST OF TABLES ...... xi

ACKNOWLEDGEMENTS ...... xii

Chapter 1 Introduction: Langmuir-Blodgett Films and TOF-SIMS Analysis ...... 1

1.1 Langmuir-Blodgett Films – a Biological Model System ...... 2 1.1.1 Monolayer at the air-water interface ...... 2 1.1.2 Supported LB films ...... 5 1.2 TOF-SIMS – Moving Towards Bioanalysis ...... 8 1.2.1 Chemical imaging ...... 10 1.2.2 Molecular depth profiling ...... 11 1.2.3 Instrumentations ...... 13 1.3 References ...... 13

Chapter 2 Investigating Lipid-lipid Interactions by TOF-SIMS Imaging ...... 16

2.1 Introduction ...... 16 2.2 Experimental Section ...... 17 2.2.1 Materials ...... 17 2.2.2 Substrate Preparation ...... 18 2.2.3 LB film preparation ...... 18 2.2.4 Instrumentation and data analysis ...... 19 2.3 Results and Discussion ...... 21 2.3.1 Lipid domains observed by SIMS ...... 21 2.3.2 Cholesterol interactions with phospholipids ...... 25 2.3.3 Quantification of lipid content ...... 26 2.4 Conclusions ...... 30 2.5 Acknowledgement ...... 31 2.6 References ...... 31

Chapter 3 Mass Spectrometric Imaging of Membrane Proteins in a Model Langmuir-Blodgett Membrane System ...... 34

3.1 Introduction ...... 34 3.2 Experimental Section ...... 37 3.2.1 Materials ...... 37 3.2.2 LB film construction ...... 37 3.2.3 Sample preparation for matrix effect study ...... 39 3.2.4 TOF-SIMS analysis ...... 40

v 3.2.5 Data analysis ...... 40 3.3 Results and Discussion ...... 41 3.3.1 Reference LB films of lipids ...... 41 3.3.2 Evaluation of possible matrix effect ...... 45 3.3.3 GpA reference LB film ...... 48 3.3.4 Outer membrane leaflet mimic LB film (DPPC/cholesterol/GpA) ...... 48 3.3.5 Inner membrane leaflet mimic LB film (DPPE/Cholesterol/GpA) ...... 50 3.3.6 Principal component analysis ...... 52 3.4 Conclusions ...... 57 3.5 Acknowledgements ...... 59 3.6 References ...... 59

Chapter 4 Chemically Alternating Langmuir-Blodgett Multilayer Films as a Model for Molecular Depth Profiling ...... 62

4.1 Introduction ...... 62 4.2 Experimental Section ...... 64 4.2.1 Materials ...... 64 4.2.2 Substrate and LB film preparation ...... 65 4.2.3 Instrumentation ...... 66 4.2.4 Ellipsometry and AFM measurements ...... 67 4.3 Results and Discussions ...... 67 4.3.1 LB film characterisitics ...... 67 4.3.2 Characterization of LB films by SIMS ...... 71 4.3.3 Calculation of depth resolution ...... 75 4.4 Conclustions ...... 76 4.5 Acknowledgement ...... 77 4.6 References ...... 77

Chapter 5 Molecular Depth Profiling of Multilayer Langmuir-Blodgett Films to Investigate Optimal Depth Resolution ...... 80

5.1 Introduction ...... 80 5.2 Experimental Section ...... 83 5.2.1 Materials ...... 83 5.2.2 Substrates and film preparation ...... 83 5.2.3 Instrumentation ...... 84 5.2.4 Ellipsometry and AFM measurement ...... 85 5.3 Results and Discussions ...... 86 5.3.1 Single component LB films ...... 86 5.3.2 Multilayer structures ...... 91 5.3.3 Surface Topography ...... 95 5.3.4 Primary ion energy and incident angle effects ...... 100 5.4 Conclusions ...... 105

vi 5.5 Acknowledgement ...... 107 5.6 References ...... 107

Chapter 6 Three-dimensional Imaging of Alternating Langmuir-Blodgett Films for Retrospective Analysis ...... 111

6.1 Introduction ...... 111 6.2 Experimental Section ...... 112 6.2.1 Materials and film preparation ...... 112 6.2.2 Three dimensional imaging and data processing ...... 113 6.3 Results and Discussion ...... 114 6.3.1 Influence of raster mode ...... 115 6.3.2 The effect of data acquisition range and position on interface width ... 118 6.4 Conclusions ...... 124 6.5 Acknowledgement ...... 125 6.6 References ...... 125

Chapter 7 Conclusions and Future Direction ...... 127

vii LIST OF FIGURES

Figure 1-1: Photograph of a Kibron µ-Trough S-LB (Kibron, Helsinki, Finland) which is used for LB film preparation. The apparatus is placed in a plexiglass box against dust and contaminations. The size of the apparatus is shown by the ruler placed with it...... 3

Figure 1-2: (a) Schematic isotherms of typical fatty acids and phospholipids, (b) Orientation of molecules at the air-water interface under different phases...... 5

Figure 1-3: Schematic drawing showing the formation and structure of supported monolayer lipid films...... 6

Figure 1-4: Schematic drawing showing the formation of LB multilayer films with the left column depicting the molecular organization...... 8

Figure 2-1: Secondary ion mass spectra of supported LB films: (a) 23%CH/47%SSM/30%POPC, (b) 23%CH/47%OSM/30%PSPC...... 22

Figure 2-2: Molecular structures of (a) CH, (b) SSM, (c) OSM, (d) PSPC, and (e) POPC...... 22

Figure 2-3: TOF-SIMS spectrum and images of the substrate: self-assembled monolayer (SAM) of 16-mercaptohexadecanoic acid on Au. The scale bar represents 100 µm. The images are 256 x 256 pixels with 20 shots/pixel. (a) Mass spectrum of the substrate, (b) SIMS image of Au (m/z 197), (c) SIMS image of SAM (m/z 340)...... 23

Figure 2-4: TOF-SIMS images of the 4 supported lipid 3-component LB films. The scale bar represents 100 µm. All the total ion images and molecular ion images for CH/SSM/PSPC and CH/OSM/POPC films are 256 x 256 pixels and the molecular specific images for CH/OSM/PSPC and CH/SSM/POPC films are 128 x 128 pixels, with 40 shots/pixel. CH (blue), PC (green), and SM (red or pink) are represented by m/z 369, m/z 224, and m/z 264 respectively. The line scans shown below represent the intensity variation along the yellow arrows superimposed on the SIMS images, both with respect to the length and the direction...... 24

Figure 2-5: TOF-SIMS images of a CH/SSM/POPC film. The scale bar represents 100 µm. (a) The total ion image is 256 x 256 pixels and (b) the molecular specific images are 64 x 64 pixels, with 40 shots/pixel. CH (blue), PC (green), and SM (red or pink) are represented by m/z 369, m/z 224, and m/z 264 respectively. (c) The line scans represent the intensity variation

viii along the yellow arrows superimposed on the SIMS images, both with respect to the length and the direction...... 28

Figure 3-1: Surface pressure – area isotherms for inner and outer membrane leaflet LB mimics. The outer leaflet plot is displaced upward by ∼ 0.5 nN m-1 for purposes of visual clarity...... 39

Figure 3-2: TOF-SIMS spectra of (A) GpA LB film, (B) DPPE/cholesterol LB film and (C) DPPC/cholesterol LB film with SIMS peaks attributable to their components labelled. The spectra are all collected under the same operating conditions, described in the text, and as such the intensity scales are comparable...... 44

Figure 3-3: (a) The expected secondary ion yield for DPPC, cholesterol and GpA based upon pure yield and molar ratio (green) and the measured yield observed from the DPPC ternary mixture (blue). (b) The expected secondary ion yield for DPPE, cholesterol and GpA based upon pure yield and molar ratio (green) and the measured yield observed from the DPPE ternary mixture (blue) ...... 47

Figure 3-4: Mass spectral images of GpA LB film ...... 48

Figure 3-5: Mass spectral images of DPPC/cholesterol/GpA LB film with m/z 184 representing DPPC, m/z369 representing cholesterol, and m/z 59 and m/z 72 representing GpA...... 49

Figure 3-6: Mass spectral images of the DPPE/cholesterol/GpA LB film with m/z 551 representing DPPE and m/z 369 representing cholesterol...... 51

Figure 3-7: Mass spectral images of the DPPE / cholesterol / GpA LB film showing peaks attributable to amino acids ...... 51

Figure 3-8: Principal component 1 scores plot for the DPPE / cholesterol / GpA. The total ion image associated with this data is shown in Figure 6...... 53

Figure 3-9: Loading plots for principal component 1 (a) m/z 1 – 1000, (b) m/z 0 – 200, (c) m/z 360 – 400 and, (d) m/z 545 – 560...... 54

Figure 4-1: Schematic drawing of 3 alternating Langmuir-Blodgett films with thickness of each block and number of layers listed...... 68

Figure 4-2: (a) Optical image of LB20 film with a crater in the middle which is + created after C60 depth profiling (the crater is the grey area which is surrounded by blue uneroded area), (b) AFM measurements of LB20 films + with a crater which is formed by C60 depth profiling...... 70

ix + Figure 4-3: Chemical structures and C60 -induced mass spectrum of LB monolayer. (a) AA, and (b) DMPA. Both spectra have Ba+ at m/z 138 and BaOH+ at m/z 155. AA has characteristic peaks at m/z 463 and 471, while DMPA is characterized by peaks m/z 355, 371, and 525...... 72

+ Figure 4-4: C60 ion fluence dependence of AA, DMPA, and Si signals of (a) LB20, (b) LB12, and (c) LB6 films. AA, DMPA, and Si are represented by m/z 463, m/z 525, and m/z 112, repectively...... 74

Figure 4-5: The plot of contrast versus layer thickness (d) over interface width (Δz)...... 76

Figure 5-1: Depth profiles of single component LB films of (a) 105 nm AA, and (b) 96 nm DMPA deposited on piranha etched silicon substrates. Sputter + erosion and data acquisition was performed using 40-keV C60 projectiles. Darker lines denote profiles measured at room temperature (R.T.) and brighter colored lines represent profiles measured at liquid nitrogen (LN2) temperature. Note that m/z 463 was not observed in DMPA spectrum and m/z 525 was observed in AA spectrum...... 88

Figure 5-2: (a) the chemical structure of the alternating LB film of AA and DMPA deposited on piranha etched silicon substrate and the depth profiles measured at (b) room temperature and (c) liquid nitrogen temperature using + 40 keV C60 projectiles...... 92

Figure 5-3: Total sputter yield vs. primary ion fluence during depth profiling through alternating LB multilayer film. The data were normalized to the value at the beginning of the depth profile...... 94

Figure 5-4: Depth profiles of alternating LB film of AA and DMPA deposited on silicon substrate cleaned with (a) ozone treatment and (b) methanol + sonication measured at liquid nitrogen temperature using 40-keV C60 projectile ions...... 97

Figure 5-5: Interface width vs. eroded depth for alternating LB films with different initial surface roughness. Straight lines: linear least squares fit for each film. Error bars correspond to ±5% of the calculated value...... 99

Figure 5-6: Depth profiles of alternating LB film of DMPA and AA deposited on ozone-treated substrate measured at liquid nitrogen temperature using (a) 20 + 2+ keV C60 and (b) 80 keV C60 projectile ions...... 101

Figure 5-7: (a) Interface width increment with depth for alternating LB films (ozone treated substrates) for different primary ion energy, and (b) Interface

x width at zero depth plotted against primary ion energy. The error bars are ±5% of the calculated value...... 103

Figure 5-8: Depth profiles of alternating LB film of DMPA and AA deposited on ozone-treated Si substrate measured at liquid nitrogen temperature using 40- + keV C60 projectiles impinging under (a) 73° and (b) 5° with respect to the surface normal...... 105

Figure 6-1: (a) Schematic drawing of the alternating LB film for three- dimensional imaging experiment, (b) three-dimensional representation of the alternating LB film reconstructed from TOF-SIMS data with external sputtering, (c) three-dimensional representation of the alternating LB film reconstructed from TOF-SIMS data with TV sputtering. For (b) and (c), the DMPA signal is depicted in green, the AA signal in red, and Si substrate signal in blue...... 117

Figure 6-2: (a) Schematic drawing to show the location of corresponding depth profiles displayed in (b) to (f) in the original three-dimensional image. The DMPA signal is depicted in green, the AA signal in red, and Si substrate signal in blue...... 119

Figure 6-3: Depth profiles with different field-of-view (FOV) extracted from external-sputtered three-dimensional image (figure 1(b)). The DMPA signal is depicted in green, the AA signal in red, and Si substrate signal in blue...... 121

Figure 6-4: (a) Interface width from depth profiles extracted from different field- of-view (FOV) are plotted against depth, (b) Interface width ...... 122

xi LIST OF TABLES

Table 2-1: The relative sensitivity factors (RSF) for each of the lipid components in the single, two, and three component lipid LB films. All the calculations included at least 3 measurements of different areas in 1 or 2 samples ...... 29

Table 2-2: The concentration of each of the lipid components within and outside the cholesterol domains of Figure 5. Concentration was determined in (a) using the RSF values for the two-component systems, and in (b) using the RSF values for the three-component system. Note that the error of concentration arises from the RSF value used in the calculation...... 30

Table 3-1: Diagnostic fragment ions from cholesterol, DPPC and DPPE that are present in DPPC / cholesterol and DPPE / cholesterol films...... 42

Table 3-2: Amino acid molecular weights and common mass spectral ions compiled from references [22,23,24]. Formulas are shown where given...... 43

xii ACKNOWLEDGEMENTS

One of the Chinese characters in my first name, “Lei”, means radium in English.

This character is given by my father with a hope that I will become a successful woman as Marie Curie who discovered radium. Whether I will be that successful remains unknown, yet, I have made another important achievement towards my father’s hope— obtaining my Ph.D degree in chemistry. I would like to take this opportunity to extend my thanks to everyone who has offered me help to make this moment happen.

First of all, I would like to express my sincere gratitude to my research advisor,

Prof. Nicholas Winograd for his guidance and support. He has provided a free yet effective environment for scientific research. He is always there when I need some help, no matter what it is. Nick, thank you so much for your trust, patience, and encouragement. I have learned so many from you, on science, writing, communication, and even personal skills. Joining your laboratory is one of the most correct decisions I have made in my life.

I extend my thanks to my committee members, Prof. Barbara Garrison, Prof.

Andrew Ewing, Prof. Christine Keating, and Prof. Ahmed Heikal for their help and guidance throughout these years. My special thanks go to Prof Andreas Wucher from

University of Duisburg-Essen, Germany, who is a visiting scholar at our laboratory several times every year. The work in Chapter 5 and 6 is the result of collaboration with him. Andreas, thank you so much for all the inspiring ideas and insightful discussions.

Your excitement about science really impresses me. I feel very lucky to know you.

xiii I wish to thank all my present and past colleagues and friends from the Winograd group who have helped and supported me over the years, Daniel Brenes, Dr. Juan Cheng,

Caiyan Lu, Dr. Joseph Kozole, Andrew Kucher, Michael Kurczy, Dan Mao, Dr. Carolyn

McQuaw, Dr. Sara Ostrowski, Dr. Shawn Perry, Paul Piehowski, Dr. Edward Smiley, Dr.

Christopher Szakal, Dr. Audra Sostarecz, David Willingham, and Dr Zihua Zhu. I do have to say a few words to the following people. Carrie – I really appreciate your guidance on the Langmuir-Blodgett project; your motivation and hard work has always impressed me; it has been a great experience working with you, and thank you for being my friend. Juan and Caiyan – it is so nice to have you two in the lab, my graduate school life would have been so different without knowing you. Mike – I always enjoy talking to you and thank you for all your consideration; you are a great man and best wishes to you and Kate. Zihua – thank you for all the help and your compliment; it is really fun talking to you. Chris and Joe – thank you for fixing the instrument and patiently teaching me everything about the instruments. Ed – you always have smile on your face just like your last name; thank you for all the computer and network fix. Dan – my admire to you is like the water of Yangzi River, which never stops running, you know what I mean; really glad to know you. Shawn – you are one of the nicest persons I have ever known and just like the TV character you always remind me of: “everybody loves you”. I extend thanks to Prof. David Allara’s group for letting me use their experimental resources, Prof. Erin

Sheets group for the collaborations. I also want to thank some members from Prof.

Mallouk’s group, including Yanyan Cao, Dr. Mihalu Eguchi, Hideo Hata and his wife,

xiv Anna Lee, and Yang Wang and her husband Shito Fei. Anna, it is really great to know you at Penn State and we will always be good friends.

I owe special thanks to our staff assistant Sabrina Glasgow. Sabrina, thank you for all the help on paper works and other issues. Whenever I turn to you for help, you always solved the problem for me. Thank you for being considerate and I really enjoy talking to you too.

Last but not least, I want to thank my family. I owe this thesis and myself to my parents, Shixian Zheng and Yinhui Jiao. Dear Mum and Dad, thank you for all the unconditional love you have given me. I hope you have been, are, and will be proud of me. Dear grandma (Wai Po), thank you for raising me up and for all the delicious food you have cooked for me. I regret so much that I didn’t go back to China to see you more before you passed away. Whenever I think of that, I just cannot stop crying. You are always in my heart, always. Finally to my dear husband, Yoji, thank you for your loving support on all aspects and please keep on doing that. I am sure we will have bright future together.

Chapter 1

Introduction: Langmuir-Blodgett Films and TOF-SIMS Analysis

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is one of the major techniques for the surface characterization of solids. With its high sensitivity for chemical information of complex materials, the range of its application has been expanding fast. Recently, there has been tremendous interest in applying TOF-SIMS to the analysis of biological systems, e.g. cells and tissues, because of its unique chemical imaging capability without the requirement of any labeling. With the development of cluster primary ion sources for SIMS, depth profiling through organic and biological systems with minimum chemical damage has also become feasible. The combination of chemical imaging with molecular depth profiling has led to the concept of three- dimensional mass spectral imaging by TOF-SIMS. However, biological systems are usually complex in chemical contents and require special sample treatments for analysis in the ultra-high vacuum environment. Model systems that can mimic cellular membranes or other biological systems are required to explore and develop the capability of TOF-SIMS for biological analysis. This thesis focuses on using Langmuir-Blodgett

(LB) films of lipid molecules as such a model. In this chapter, the basics of LB films and recent development of TOF-SIMS bio-analysis will be briefly introduced, together with general experimental methods and instrumentation of TOF-SIMS.

2 1.1 Langmuir-Blodgett Films – a Biological Model System

A LB film is a set of monolayers deposited on a solid substrate, consisting of a single layer or many layers, up to a depth of several visible light wavelengths. The LB technique is a well-established and sophisticated method to control interfacial molecular orientation and packing. It was first introduced by Irving Langmuir1 and applied extensively by Katherine Blodgett2,3, after whom the technique is named. The method has been widely applied in the fabrication of sensors, detectors, displays, and electronic circuit components. The possibility to organize organic molecules, almost without limitations, with desired structure and functionality in conjunction with a sophisticated thin film deposition technology enables the production of electrically, optically and biologically active components on a nanometer scale. Molecules known to form LB films include fatty acids and their derivatives, molecules containing five or six-membered rings, porphyrins and phthalocyanines, and some polymers.4 This thesis is focused on LB films formed from lipid molecules and fatty acids as model cell membrane systems.

These lipid films have well-controlled chemical contents and organized chemical structures. These properties, together with vacuum stability, make lipid LB films a well- suited model for TOF-SIMS bioanalysis.

1.1.1 Monolayer at the air-water interface

Lipids and fatty acids are amphiphilic molecules which consist of a hydrophilic and a hydrophobic part. They form insoluble monolayers at an air-water interface, from which the LB films are transferred onto a solid support. A Langmuir-Blodgett trough,

3 which was first described by Langmuir in 1917,1 is required to prepare these monolayers.

The trough used for film preparation in this thesis is a Kibron µTrough S-LB (Kibron,

Helsinki, Finland) as shown in Figure 1-1 . The glass trough with Teflon edges holds 60-

70 mL subphase liquid (water or aqueous solutions) and has a surface area of 59 mm x

202 mm. The two movable Teflon barriers control the area of the monolayer.

Deposition Glass Trough Substrate Apparatus

Wilhelmy Wire

Barriers

The lipids and fatty acids are dissolved in a volatile water-insoluble solvent, such as chloroform, iso-propanol, hexane, and methanol or combinations of two of these solvents. The solution is then applied dropwise onto the air-water interface by a micro syringe. After solvent evaporation, the monolayer is compressed by the two Teflon barriers at a constant rate. During the compression, the surface pressure (mN/m) is

4 measured through the Wilhelmy wire interfaced to a personal computer. The plot of surface pressure as a function of area per molecule at a constant temperature is known as a surface isotherm which is the most important indicator of the monolayer properties of the amphiphilic molecules.5 A number of distinct regions are apparent on examining the isotherm, which are called phases. When a monolayer is compressed, it passes though several different phases which are marked by discontinuities in the isotherm. The phase behavior of the isotherm is determined by the physical and chemical properties of the amphiphile, the subphase temperature and the subphase composition.6

Schematic isotherms of a typical fatty acid and a phospholipid are shown in

Figure 1-2 . A simple terminology used to classify different monolayer phases of fatty acids has been proposed by W.D. Harkins as early as 1952.7 At large molecular areas, the monolayers exist in the gaseous state (G) and on compression undergo a phase transition to the liquid-expanded state (L1). Upon further compression, the L1 phase undergoes a transition to the liquid-condensed state (L2), and at even higher densities the monolayer finally reaches the solid state (S). If the monolayer is further compressed after reaching the S state the monolayer will collapse into three-dimensional structures. The collapse is generally seen as a rapid decrease in the surface pressure or as a horizontal break in the isotherm if the monolayer is in a liquid state. Following the definitions above, one can see that fatty acids have three distinct regions; gas (G), liquid (L1) and solid (S), while the phospholipid has an additional almost horizontal transition phase (L2-

L1) between the two different liquid phases. This is common for phospholipids and the position of this horizontal transition phase is temperature-dependent. As the temperature

5 is increased the surface pressure value at which the horizontal transition phase occurs will increase, and vice versa.

(a) (b) Solid phase (S) 60 Fatty acid Phospholipid H2O 50 S S Liquid phase (L) 40

H2O 30 L2 L1+L2 20

Surface Pressure (mN/m) Gas phase (G) 10 L1 L1

G G H2O 0 Area/molecule (Å2) Figure 1-2: (a) Schematic isotherms of typical fatty acids and phospholipids, (b) orientation of molecules at the air-water interface under different phases.

1.1.2 Supported LB films

The monolayer at the air-water interface can be transferred onto a solid substrate in a layer-by-layer fashion to form supported LB films, a procedure first described by

Katherine Blodgett.2 The substrate is lifted vertically through the air-water interface for monolayer transfer. The substrates used for LB films in this thesis are all hydrophilic; thus the molecules orient with their hydrophilic group attached to the substrate. Two types of supported LB films are discussed in the thesis; monolayer film and multilayer films. Supported monolayer films are used for the purpose of TOF-SIMS chemical

6 imaging (Chapter 2 and 3). The substrate is an acid-terminated self-assembled monolayer on gold. This substrate has been shown to enhance the SIMS signal of lipid molecules.8 A schematic diagram of supported monolayer film construction is shown in

Figure 1-3. The film transfer can be done at any point of the isotherm except in the gas phase. This allows us to select the surface pressure or molecular area at which the monolayer best represents the real cellular membrane. The surface pressure is kept constant during film transfer. The monolayer films are formed from phospholipids, sphingomyelin, and cholesterol or combinations of these molecules to mimic one leaflet of the cellular membrane (Chapter 2). This model system simplifies the chemical content while maintaining the essential components, which makes it possible to study specific lipid-lipid interactions. Integral membrane proteins can be incorporated into the monolayer by direct mixing with lipids in the solvent before applying onto the air-water interface as long as they are soluble in the organic solvents (Chapter 3). The formation of the monolayer on the substrate is confirmed by ellipsometry measurements of the film thickness.

Figure 1-3: Schematic drawing showing the formation and structure of supported monolayer lipid films.

7 While supported monolayer films can be formed for most lipid molecules and fatty acids, the formation of stable multilayer films is only limited to fatty acids and lipids with acid terminated headgroups, e.g. phosphatidic acid (PA), and the film transfer must be done at high surface pressure. The mechanism of how multilayers are formed on the solid substrates remains unclear. The deposition of the first layer is quite critical and a strongly bound first layer is preferred for successfully subsequent deposition.4

The multilayer films built in this thesis include arachidic acid (AA), dimyristoyl phosphatidic acid (DMPA), and alternating multilayer films of AA and DMPA. It is important to point out that the multilayer of DMPA does not form by itself but forms on substrates with 3 layers of AA. The AA layers functions as a foundation for additional multilayers. Divalent heavy metal ions are included in the subphase and the pH value of the subphase is adjusted to be slightly more than seven, which ensure that the acid molecules form salts with the metal ions at the air-water interface and are transferred in the salt form. It is possible that the electrostatic interaction associated with salt formation stabilizes the multilayer films. The formation of the multilayer is schematically depicted in Figure 1-4. The first layer has its hydrophilic headgroup facing the substrate and the following layers form in a head-to-head and tail-to-tail fashion. The multilayer can be built up to several nanometers and the color of the film changes with thickness due to light interference. These multilayer films, especially the alternating ones, have well- organized chemical structures and sharp interfaces, which make them a valuable model for fundamental studies of SIMS molecular depth profiling, as discussed in Chapter 4, 5, and 6.

1st layer

2nd layer

3rd layer

Figure 1-4: Schematic drawing showing the formation of LB multilayer films with the left column depicting the molecular organization.

1.2 TOF-SIMS – Moving Towards Bioanalysis

Mass spectrometry has become a widely used and powerful bioanalytical technique especially since the discovery of the two popular ionization methods, matrix- assisted laser desorption ionization (MALDI) and electrospray ionization (ESI).9 SIMS is a unique mass spectrometric technique which has high surface sensitivity and imaging capability. Recently, there is tremendous interest in applying TOF-SIMS to the analysis of biological samples especially after the discovery of cluster projectiles. TOF-SIMS is

9 complimentary to MALDI imaging due to higher image resolution and less interference at the low mass region.

Secondary ion mass spectrometry is traditionally used for inorganic material characterization and depth profiling. The samples are ionized by a beam of energetic ions, which bombard the sample surface in the experiments. The energy transfer leads to ionization of the top layer of the sample and ions representing the surface composition are desorbed into vacuum. The bombarding ions are called primary ion beam and the emitted ions are referred to as the secondary ions. The secondary ions are sent to the mass analyzer to produce mass spectra which contain elemental and molecular information of the surface. Detailed information about SIMS is available, including basic concepts, instrumentation, and applications.10

SIMS can be divided into two types, dynamic SIMS and static SIMS depending on the primary ion dose. In dynamic SIMS, the primary ion beam bombards the sample continuously and elemental information is monitored as a function of depth. Dynamic

SIMS is typically used in the semiconductor industry for elemental analysis. In static

SIMS, however, the primary ion dose is kept sufficiently low such that the first monolayer is left undisturbed and the mass spectra do not change within the analysis time.

The TOF mass analyzer is typically used for static SIMS mainly due to its substantially high transmission efficiency (>50%)11. It is widely accepted that 1012 primary ions/cm2 is the static limit with the traditional atomic primary ion projectiles. It is particularly important to maintain the primary ion dose below the static limit for SIMS analysis of biological samples since if the surface is damaged by energetic ion bombardment, the molecular information will no longer represent the original chemistry. However, this

10 static limit is not applicable to the quickly developing cluster ion sources, which will be discussed later in the next section.

1.2.1 Chemical imaging

One the most important features of SIMS is its ability to acquire molecule- specific images of the sample. By rastering the primary ion beam across the sample surface, mass spectra can recorded at each pixel and chemical composition of the sample surface is mapped. When it is applied to biological samples, molecule-specific pictures of the surface can be obtained without any chemical label. SIMS imaging has been successfully applied to cell and tissue imaging. In order to obtain the correct information of biological samples, special sample preparation is required to preserve the samples in their original state and viable under the ultra-high vacuum environment. Freeze drying in a trehalose medium and freeze-fracturing are considered to be the most applicable and best methods so far.12,13 However, these methods are time-consuming and still introduce artifacts. Furthermore, the chemical content of these systems is complex and unpredicted, which makes it difficult sometimes to extract core information or focus on a specific interaction. Model systems, such LB films mimicking the cellular membrane, do not require special sample treatment and the chemical content is controllable. It provides a similar molecular environment and works as a bottom-up approach to study the cellular membranes. Specific interactions between molecules, i.e. lipid-lipid and lipid-protein interactions, can be studies in the model system and such information compliments to

11 TOF-SIMS imaging of real systems. These approaches are discussed in detail in Chapter

2 and 3.

With atomic projectiles, as the pixel size approaches submicrometer dimensions, the number of molecules available for imaging becomes too small for enough signal to be acquired within the static limit. In order to obtain enough secondary ion signal without destroying the sample, secondary ion yields need to be enhanced. The recent discovery of cluster ion projectiles seems to have resolved the problem. Cluster ion bombardment was first studied in 1989.14 Secondary ion yields were enhanced to a large extent,

- especially for organic molecule-ions with SF6 bombardment. Other types of cluster

+ 15 + 16 + 17;18 + projectiles were developed after that, including Aun (n =1-5), C60 , SF5 , and Bin

(n = 1-7)19. The cluster ion beams sputter the sample with a much higher yield than the atomic projectiles, which allows the molecule-ion signal to be retained under high dose bombardment.20,21 The use of cluster ion sources has enhanced the capability of TOF-

SIMS imaging and expanded its applications.

1.2.2 Molecular depth profiling

The discovery of cluster ion projectiles not only enhances TOF-SIMS imaging capabilities, but also makes molecular depth profiling possible. Depth profiling is not a new concept in the SIMS field. It involves collecting mass spectra and monitoring peaks of interest as a function of sample depth. It is traditionally used in dynamic SIMS for elemental analysis of semiconductors. Depth profiling was made possible for molecular solids since the cluster projectiles have a much higher sputter yield than atomic

12 projectiles and the chemical damage can be removed almost as fast as it accumulates under high dose cluster bombardment. Among all the cluster projectiles, buckminsterfullerene or C60 is the most promising for molecular depth profiling purposes.9

There have been many successful examples of molecular depth profiling for various sample systems.22-27 Most of the studies, however, lack quantitative understanding of the process which is essential to further development. Recently, experimental approaches intended for quantitative evaluation of molecular depth profiling have started to appear. In our lab, an erosion model has been developed to describe the change of molecular ion intensities with fluence based upon depth profile data for spin-casted trehalose films.28 The model is built upon the balance between sputtering and damage. It has also been successfully used to explain the effect of the incident angle of the cluster projectiles during the depth profiling of vapor-deposited cholesterol films.29 A similar approach was done by a group in the UK.30,31 They used a platform of Irganox thick films and quantitatively studied the performance of organic delta layers.

One question remaining unclear is the depth resolution during molecular depth profiling. A model system with minimum organic-organic interface mixing is required to achieve quantitative evaluation of beam-induced mixing. Alternating LB multilayer films of AA and DMPA provide such a model, which is discussed in detail in Chapter 4.

In Chapter 5, this model is used again to quantitatively study how experimental parameters affect the interface width. Finally it is used as a model for three dimensional image analysis in Chapter 6. Three dimensional imaging is a combination of SIMS

13 imaging and molecular depth profiling. By recording mass spectral images as a function of depth, the chemical composition of the sample can be viewed in three dimensions.

1.2.3 Instrumentations

There are several commercially available TOF-SIMS instruments in the market.

The instruments used in this thesis were built in our lab and are described in detail in a published work.32 There have been many modifications to the instrument since then.

Two instruments are used in this thesis, BIOTOF I and BIOTOF II. They are identical in

+ + almost every part except BIOTOF I is equipped with a 40-keV C60 and 20-keV Aun (n

= 1-3) as the primary ion sources while BIOTOF II has a 25-keV Ga+ liquid metal ion gun (LMIG). BIOTOF II is used mainly for TOF-SIMS imaging of LB monolayer films in Chapter 2 and 3, while BIOTOF I is applied to molecular depth profiling and the three dimensional imaging experiments in Chapter 4, 5 and 6.

1.3 References

1. Langmuir, I. J.Am.Chem.Soc. 1917, 39, 1848-906.

2. Blodgett, K. B. J.Am.Chem.Soc. 1935, 57, 1007-22.

3. Blodgett, K. B. J.Phys.Chem. 1937, 41, 975-84.

4. Roberts, G. Langmuir-Blodgett Films, Plenum Press: New York: 1990.

14 5. Ulman, A. An Introduction to Untrathin Organic Films from L-B to Self Assembly,

Acad. Press Inc.: San Diago: 1991.

6. Petty, M. C. Langmuir-Blodgett Films: An Introduction, Cambridge University

Press: New York: 1996.

7. Harkins, W. D. Physical Chemistry of Surface Films, Reinhold, New York: 1952.

8. Sostarecz, A. G.; Cannon, D. M.; Mcquaw, C. M.; Sun, S. X.; Ewing, A. G.;

Winograd, N. Langmuir 2004, 20, 4926-32.

9. Winograd, N. Anal.Chem. 2005, 77, 142A-9A.

10. Benninghoven, A.; Werner, H. W.; Rudenauer, F. G. Secondary Ion Mass

Spectrometry: Basic Concepts, Instrumental Aspects, Applications, John Wiley &

Sons, New York: 1987.

11. Cotter, R. J. Time-of-Flight Mass Spectrometry: Instrumentation and Applications n

Biological Research, The American Chemical Society, Washington D. C.: 1997.

12. Sostarecz, A. G.; Mcquaw, C. M.; Ewing, A. G.; Winograd, N. J.Am.Chem.Soc.

2004, 126, 13882-83.

13. Parry, S.; Winograd, N. Anal.Chem. 2005, 77, 7950-57.

14. Appelhans, A. D.; Delmore, J. E. Anal.Chem. 1989, 61, 1087-93.

15. Benguerba, M.; Brunelle, A.; Dellanegra, S.; Depauw, J.; Joret, H.; Lebeyec, Y.;

Blain, M. G.; Schweikert, E. A.; Benassayag, G.; Sudraud, P. Nuclear Instruments

& Methods in Physics Research Section B-Beam Interactions with Materials and

Atoms 1991, 62, 8-22.

16. Schweikert, E. A.; van Stipdonk, M. J.; Harris, R. D. Rapid Commun.Mass

Spectrom. 1996, 10, 1987-91.

15 17. Gillen, G.; Roberson, S. Rapid Commun.Mass Spectrom. 1998, 12, 1303-12.

18. Kotter, F.; Benninghoven, A. Appl.Surf.Sci. 1998, 133, 47-57.

19. Touboul, D.; Kollmer, F.; Niehuis, E.; Brunelle, A.; Laprevote, O. J.Am.Soc.Mass

Spectrom. 2005, 16, 1608-18.

20. Postawa, Z.; Czerwinski, B.; Szewczyk, M.; Smiley, E. J.; Winograd, N.; Garrison,

B. J.Anal.Chem. 2003, 75, 4402-07.

21. Postawa, Z.; Czerwinski, B.; Szewczyk, M.; Smiley, E. J.; Winograd, N.; Garrison,

B. J. J.Phys.Chem.B 2004, 108, 7831-38.

22. Sostarecz, A. G.; Mcquaw, C. M.; Wucher, A.; Winograd, N. Anal.Chem. 2004, 76,

6651-58.

23. Wucher, A.; Sun, S. X.; Szakal, C.; Winograd, N. Anal.Chem. 2004, 76, 7234-42.

24. Cheng, J.; Winograd, N. Anal.Chem. 2005, 77, 3651-59.

25. Mahoney, C. M.; Roberson, S. V.; Gillen, G. Anal.Chem. 2004, 76, 3199-207.

26. Wagner, M. S. Anal.Chem. 2005, 77, 911-22.

27. Jones, E. A.; Lockyer, N. P.; Vickerman, J. C. Anal.Chem. 2008, 80, 2125-32.

28. Cheng, J.; Winograd, N. Appl.Surf.Sci. 2006, 252, 6498-501.

29. Kozole, J.; Wucher, A.; Winograd, N. Anal.Chem. 2008, submitted.

30. Shard, A. G.; Brewer, P. J.; Green, F. M.; Gilmore, I. S. Surf.Interface Anal. 2007,

39, 294-98.

31. Shard, A. G.; Green, F. M.; Brewer, P. J.; Seah, M. P.; Gilmore, I. S. J.Phys.Chem.B

2008, 112, 2596-605.

32.Braun, R. M.; Blenkinsopp, P.; Mullock, S. J.; Corlett, C.; Willey, K. F.; Vickerman,

J. C.; Winograd, N. Rapid Commun.Mass Spectrom. 1998, 12, 1246-52.

Chapter 2

Investigating Lipid-lipid Interactions by TOF-SIMS Imaging

This chapter has been reproduced with permission from L. Zheng, C.M. McQuaw,

A.G. Ewing, and N. Winograd, Journal of the American Chemical Society 129 (2007)

15730-15731. Copyright 2007 by the American Chemical Society. This paper was submitted as a communication and has been expanded for further clarification. This work was done in collaboration with co-author Carolyn M. McQuaw.

2.1 Introduction

Cell membranes are composed of a complex array of lipids, which play diverse roles in membrane dynamics, protein regulation, and signal transduction. It is important to understand how these lipids interact with each other and with other membrane components, in order to better comprehend membrane functions. Many techniques are available to study lipid-lipid interactions such as solid-state NMR1,2, X-ray diffraction3,4, and various fluorescence related techniques5,6. Recently, time-of-flight secondary ion mass spectrometry (TOF-SIMS) has been proven useful in identification of lipids in both model membrane systems and cellular membranes.7-10 Here, we present label-free molecule-specific images which elucidate the nature of lipid-lipid interactions in three- component cellular membrane mimics. Our results show that sphingomyelin (SM) inclusion into cholesterol (CH) domains is driven by the phospholipid acyl chain

17 saturation rather than by hydrogen bonding between SM and CH. Ternary mixtures composed of CH, SM, and phosphatidylcholine (PC) are investigated as mimics of the cellular membrane. TOF-SIMS images are acquired from supported Langmuir-Blodgett

(LB) films with varying SM and PC acyl chain saturation; either, both, or neither contains one double bond at the same position. The images clearly show that acyl chain saturation is the dominating factor in determining phase separation. Quantification of lipid contents using the molecular ion images is also approached and the concentration of each lipid inside and outside the domain is determined using the concept of relative sensitivity factor.

2.2 Experimental Section

2.2.1 Materials

POPC, PSPC, OSM, cholesterol (all from Avanti Polar Lipids, Inc., Alabaster,

AL), SSM (Matreya LLC, Pleasant Gap, PA), 16-mercaptohexadecanoic acid (Sigma-

Aldrich Co., St. Louis, MO), 2-propanol, methanol, and chloroform were used without further purification. A Nanopure diamond life science ultrapure water system (Barnstead

International, Dubuque, IA) was used to purify the water used in the production of all monolayers (resistivity of 18.2 MΩ cm)

18 2.2.2 Substrate Preparation

Single crystal (100) 3 inch wafers were cut into 1 x 2 cm pieces and piranha etched (3:1 H2SO4:H2O2) (Extreme caution must be exercised when doing piranha etch.

An explosion-proof hood should be used for the experiment) before further treatment.

100 Å Cr followed by 2000 Å Au was then deposited onto clean silicon as described by

Fisher et al [10]. 1mM solution 16-mercaptohexanoic acid in 2-propanol was used to form self assembled monolayers on gold by simply immersing the substrate in the solution overnight. The formation of SAMs was confirmed with a single wavelength

Stokes ellipsometer LSE with wavelength of 632.18 nm, 1mm spot size, and 70º incidence angle (Gaertner Scienctific Co., Skokie, IL).

2.2.3 LB film preparation

LB films preparation was accomplished using a Kibron µTrough L-LB (Helsinki,

Finland). For all the experiments, the subphase was 65-70 mL room temperature purified water with resistance of 18.2 MΩ. The lipid mixtures were dissolved in 9:1 chloroform/methanol and applied onto the surface of subphase to form monolayer film at the air-water interface by microliter syringe. It took about 30 min for solvent evaporation and film equilibration and the film was compressed by two trough barriers at the rate of 7

Å2/molecule/min. The barriers were computer controlled so that uniform compression of the film and constant feedback when depositing monolayers can be achieved. The surface pressure was measured with a Wilhelmy wire interfaced to a personal computer. The lipid films were deposited vertically onto SAM substrates at 7mN/m upon first

19 compression. The pulling rate for the film deposition is 1 mm/min. The formation of LB film on the substrate was again confirmed with the ellipsometry measurement of film thickness enhancement.

There are three types of LB films depending on their lipid contents. Single component LB films contain only one lipid and include cholesterol, POPC, PSPC, SSM, and OSM. Binary LB films were made from solvent containing two lipids and include

40% POPC/60% SSM, 40% PSPC/60%SSM, 40% POPC/60% OSM, 40% PSPC/60%

OSM, 56% POPC/44% cholesterol, 56% PSPC/44% cholesterol, 67% SSM/33% cholesterol, 67% OSM/33% cholesterol. All the single component and binary films work as references to ternary LB films which contain three lipid components in the film. These films include 30% POPC/47% SSM/23% cholesterol, 30% PSPC/47% OSM/23% cholesterol, 30% POPC/47% OSM/23% cholesterol, and 30% PSPC/47% SSM/23% cholesterol.

2.2.4 Instrumentation and data analysis

A home-built imaging TOF-SIMS equipped with a 15-keV Ga+ liquid metal ion gun (Ionoptika, Southampton, UK) was used to perform the mass spectrometric imaging experiments. Detail of this mass spectrometer has been described in detail by Braun et al.ref Spectra and images were acquired at room temperature with an ion dose less than

1012 ions/cm2. No charge compensation was used throughout the experiments. Total ion images were acquired by rastering the ion beam across the sample surface and recording mass spectra at each pixel. The intensity of individual ions was plotted for molecular-

20 specific images. All images are acquired with either 20 or 40 shots/pixel, both of which have an ion dose less than 1012 ions/cm2. Normally a smaller value of shots/pixel is preferred. A larger value is sometimes used in order to achieve sufficient signal-to-noise ratio for mapping. The primary ion beam was rastered across the sample surface and mass spectra were acquired at each pixel for total ion images (256 x 256 pixels).

Molecular-specific images were obtained by mapping the ions of interest (256 x256 pixels) or by converting to 128 x 128 pixel images. The conversion is performed by summing the adjacent 4 pixels and using the one larger pixel to represent the original 4 smaller pixels. Thus the field-of-view is the same after conversion but the size of one pixel is 4 times larger. A measure of the degree of intensity variation is given by the line scans. These line scans are constructed by measuring the intensity from a 5x5 pixel square as it moves along the yellow arrow superimposed on the images. The start point and the end point of the yellow arrow correspond to the start point and the end point of the x-axis of the line scan graph, although the thickness of the yellow arrow has no significance. Note also, that a value of zero in the line scan plot does not necessarily mean that no molecules are present in this area – only that the number of molecules is below the detection limit of the SIMS technique.

21 2.3 Results and Discussion

2.3.1 Lipid domains observed by SIMS

The LB films used for investigation are 23%CH/47%SM/30%PC, and include the variants CH/SSM/POPC, CH/OSM/PSPC, CH/SSM/PSPC, and CH/OSM/POPC. The solutions of each combination were applied to the air-water interface, compressed to 7 mN/m, and then transferred onto hydrophilic substrates. This relatively low pressure is used to ensure the appearance of immiscible liquid phases and to ensure that the size of the domains is large enough for SIMS observation. Each combination was repeated in triplicate for reproducibility.

The mass spectra of CH/SSM/POPC and CH/OSM/PSPC LB films are shown in

Figure 2-1. Characteristic fragments include; [M-OH]+ at a mass-to-charge ratio (m/z)

369 for cholesterol, a sphingosine backbone fragment [C17H30ON]+ at m/z 264 for both

SMs, and a peak at m/z 224 for both PCs which is a fragment [C8H19NPO4]+ of the PC headgroup plus part of the glycerol backbone ( Figure 2-2 ). The molecular ions are: [M-

H]+ at m/z 385 for CH; [M+H]+ at m/z 761, 763 for POPC and PSPC respectively; and

M+ at m/z 729, 731 for OSM and SSM respectively. The mass spectrum of the substrate

(SAM on gold) are shown in Figure 2-3 (a) and none of substrate peaks overlap with these lipid peaks.

197 600 6000 224 (a) 184 5000 369 400 4000 385 3000 200 761 264 731 2000 0 1000 200 250 300 350 700 750 800 0 200 400 600 800 1000 2000 200 197 224 (b) 1500 100 369

Singal Intensity (counts) 1000 264 385 184 729 763 500 0 200 250 300 350 700 750 800 0 200 400 600 800 1000 m/z, positive ions

Figure 2-1: Secondary ion mass spectra of supported LB films: (a) 23%CH/47%SSM/30%POPC, (b) 23%CH/47%OSM/30%PSPC.

(a)

HO (b) O (c) O O O HN HN P + O P O + O O N O N O OH m/z 264 OH m/z 264 O O (d) (e) O O O O + O P O O + O P O O N O N O m/z 224 O m/z 224 O

Figure 2-2: Molecular structures of (a) CH, (b) SSM, (c) OSM, (d) PSPC, and (e) POPC.

(a) (b)

(c)

Since CH, SM, and PC are identified in each film by TOF-SIMS, molecule- specific images identify the location of each lipid and representative images are presented in Figure 2-4 with their total ion images. CH/OSM/POPC and CH/SSM/PSPC films are homogeneous with all lipid components evenly distributed. However, domain structures are observed for the films of CH/SSM/POPC and CH/OSM/PSPC. [Note that substrate images are displayed in Figure 2-3 (b) and (c), and the uniformity of the images confirms that there is no substrate induced domain formation.] Lipid localization is also confirmed by line scans (Figure 2-4). The molecule-specific images for the CH/SSM/POPC films show that CH is co-localized with SSM in the domain and that POPC is excluded from these areas. For CH/OSM/PSPC, however, PSPC co-localizes with the CH domains and

OSM is excluded. The secondary ion intensities of CH and the co-localized lipid are

24 close to zero outside the CH-rich domain area. However, lipid exclusion is not complete since a residual intensity is still observed in the CH-poor areas.

CH/SSM/POPC CH/OSM/PSPC CH/SSM/PSPC CH/OSM/POPC Total SM SM PC CH ) ) 2 2 14 1.0 12 0.8 10 8 0.6 6 0.4 4 0.2 2 0 0 100 200 300 400 0 50 100 150 200 Intensity (Counts x 10 (Counts Intensity Intensity (Counts x 10 Length (µm) Length (µm)

25 2.3.2 Cholesterol interactions with phospholipids

Model membranes containing CH, SM, and PC have been widely used in CH-SM interaction studies, and phase separation has been observed by fluorescence microscopy6,15 and atomic force microscopy16. In our experiments, the SMs and PCs were specifically chosen to have the same number of carbons on both acyl chains so that they only differ by the linkage of the 16-carbon chain to the headgroup and by the saturation of the other 18-carbon chain. Without the need for labels, molecule-specific images reported here show that when SM and PC are both saturated or both unsaturated all the lipids are evenly distributed in the film and CH domains do not form. Thus, CH does not differentiate between SM and PC by their head-tail linkage. However, when SM and PC differ by a double bond placed in the middle of the 18-carbon chain, CH domains are observed in the film due to phase separation, which means CH interacts with one lipid significantly more strongly than the other. Clearly, CH favors the lipid that has saturated acyl chains, and this preference is strong enough to localize the saturated lipids into CH domains and to exclude the unsaturated lipid. Cholesterol is known to have a condensing effect on other lipids, which can be explained by the hydrophobic match between the steroid ring of CH and the acyl chains of other lipids.17 Lipids with saturated acyl chains can interact more closely with CH than those with unsaturated acyl chains since the double bond produces a kink in the middle of the carbon chain that sterically prevents half of the chain from interacting with CH. Our results show that one double bond in the acyl chain is enough to change the lipid interaction with CH, regardless of the difference in the head-tail linkage region of SM and PC. The results also suggest that the SM-CH

26 interaction is dominated by the hydrophobic match of acyl chains, and that hydrogen bonding between the amide or the sphingoid of SM and the -OH group of CH does not contribute significantly to the total interaction. McConnell has proposed a condensing complex model which suggests, in a ternary mixture, the formation of “condensed complexes” between cholesterol and saturated lipids and the complex is immiscible with the unsaturated lipids.18 Our results show that CH preferentially interacts with lipids through the saturated acyl chain which may indeed indicate the formation of complexes.

However, as noted above, the exclusion of the unsaturated lipids from CH domains is not complete. Hence, if the condensing complexes form in our ternary systems, they are not

100% immiscible with the unsaturated lipids.

2.3.3 Quantification of lipid content

Figure 2-5 shows another set of images for the CH/SSM/POPC film. It would be valuable to extract quantitative compositional information directly from the molecular specific images. For mass spectrometry experiments in general19-22, and for SIMS experiments in particular23-25, ion signal intensity is not typically proportional to concentration due to what are generally referred to as matrix effects. For the system studied here, for example, it has been shown that when CH is co-localized with phosphocholine-phospholipids, proton transfer can increase the intensity of phosphocholine, ([C5H15NPO4]+, at m/z 184.25 However, there are strategies that can be employed to take into account these matrix effects, and provide at least an estimate of the composition of lipids inside and outside the CH domains shown in Figure 2-5. Our

27 approach is to calculate a relative sensitivity factor (RSF) for each of the three lipid components in the LB films. RSF is used most commonly in elemental analysis of doped materials.26-28 When the matrix elemental concentration is constant, then RSF is defined by Eq. 2-1

Ix RSFx = [Eq. 2-1] Cx * IM where, RSFx is the relative sensitivity factor for component x; Cx is the concentration of component x; IM is the secondary ion intensity of the matrix reference ion; and Ix is the secondary ion intensity for the relevant ion of component x. Number of different reference ions, including Au+ and several major peaks from 16-mercaptohexadecanoic acid SAM, were examined. We finally chose Au+ at m/z 197, since its intensity is most constant from sample to sample. The values for the single component lipid films are given in Table 2-1 . Note that the RSF value for CH is more than 50 times larger than for

SM, and 6.6 times larger than for POPC.

The magnitude of matrix effects can be discerned by calculating the RSF values for all combinations of binary components; that is 2:3 POPC/SSM, 4:3 POPC/CH, and

2:1 SSM/CH for conditions where there is no observable domain formation. The molar ratios of the lipid components in these binary systems are the same as the ratios utilized in the ternary system. For the 3-component system, the RSF values may be obtained directly from a region of the monolayer that represents the macroscopic stoichiometry.

These calculations assume that the concentrations reported for the 2- and 3-component systems are identical to the concentration of the lipid mixtures applied to the LB trough.

These values are also reported in Table 2-1. Note that the RSF values for CH are lower

28 by about a factor of 2, and the RSF values for SM are higher by about a factor of 2. These changes are consistent with the proton transfer mechanism noted above.

(b)

(a) POPC

CH 18:0 SM POPC

+ + + [M-OH] [C17H30ON] [C8H19NPO4] Sample Composition (m/z 369) (m/z 264) (m/z 224)

CH 0.72±0.1 – –

18:0 SM – 0.013±0.001 –

POPC – – 0.11±0.005

2:3 POPC/18:0 SM – 0.026±0.001 0.17±0.01

4:3 POPC/CH 0.34±0.002 – 0.13±0.01

2:1 18:0 SM/CH 0.38±0.005 0.23±0.001 –

30/47/23 POPC/18:0 SM/CH 0.31±0.003 0.021±0.002 0.21±0.02

The 2-component RSF values have been used to estimate the average concentration of each component in a 3-component film. The RSF values of the 2- component mixtures were averaged and applied to the signal intensities measured for the

3-component mass spectrum. These results are shown in Table 2-2 . The agreement between the expected values and the calculated values provides a sense of the reliability of the numbers. Similarly, using the RSF values calculated from the 2- and 3- component films, it is possible to estimate the molar concentrations of each species inside and outside the CH domains shown in Figure 2-5. Two methods were employed. In the first method (a), the 2 component RSF values were applied to the measured ion intensity inside and outside a CH domain shown in Figure 2-5. In the second method (b), the RSF

30 values of the 3-component film were applied directly to these secondary ion intensities.

The results are shown in Table 2-2. The magnitude of the numbers certainly suggest that

SSM is more concentrated in the CH domains, and that POPC is presently largely outside the CH domain, as is evident from inspection of Figure 2-5.

CH 18:0 SM POPC

+ + + 30/47/23 [M-OH] [C17H30ON] [C8H19NPO4] POPC/18:0 SM/CH (m/z 369) (m/z 264) (m/z 224)

a b a b a b

entire sample 19±2 – 43±2 – 38±2 –

within CH domains 20±2 21±2 61±2 65±6 19±1 14±1

outside CH domains 0 0 20±1 31±3 80±4 69±7

2.4 Conclusions

Using TOF-SIMS we have observed the label-free lipid localization determined by acyl chain saturation and its effect on CH domain formation. The result indicates that the high saturation level of SM acyl chains in the cellular membrane is the important driving force for SM co-localization with CH in lipid rafts. Other possible specific interactions between sphingoid or amide-linkage groups and CH are not observed.

31 Quantitative information of lipid content is extracted from the molecular specific images and concentration of CH, PC, and SM are determined inside and outside the domains.

This study has extended the use of label-free mass spectrometry imaging to understanding complex biological interactions at the molecular level.

2.5 Acknowledgement

This work is supported by the National Institute of Health under grant

#EB002016-13 and the National Science Foundation under grant #CHE-555314. The authors thank Dr. David L. Allara and his research group for the use of ellipsometry and

Dr. Erin Sheets for insightful discussion.

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Chapter 3

Mass Spectrometric Imaging of Membrane Proteins in a Model Langmuir-Blodgett Membrane System

This chapter has been reproduced with permission from Baker, M.J.; Zheng, L.;

Winograd, N.; Lockyer, N.P.; and Vickerman, J.C. Langmuir, submitted for publication.

Unpublished work copyright 2008 American Chemical Society. LB film imaging and analysis by SIMS were done at the Pennsylvania State University. The matrix effect and principle component analysis were carried out by co-author Mathew J. Baker at the

University of Manchester, UK.

3.1 Introduction

The cell membrane comprises the surface of all living cells. It is formed of a fluid lipid bilayer in which embedded proteins carry out a myriad of functions including acting as enzymes, ion pumps, transport proteins and receptors for hormones. The bilayer assembly regulates the entry and exit of most solutes and ions, with few substances being able to diffuse through unaided.1 The cell membrane is a very dynamic structure whose behavior is often described by a fluid mosaic model2 whereby all lipid or protein molecules in the biological membrane diffuse more or less freely as a two dimensional liquid. As a direct consequence, both types of molecules would be expected to be randomly distributed within the membrane. More recent experiments suggest the situation is more complex due to the occurrence of both a transverse and lateral

35 regionalization within the bilayers. The observation of micro- and macrodomains is widespread.3

Recent studies have focused upon lipids in the cellular membrane, with special emphasis placed upon elucidating their role in transport and signaling within the cell via organized lipid domains. There are many diseases that are thought to utilize cellular domains. The exit of HIV from a cell depends upon membrane rafts which contain HIV spike proteins4 and the study of Alzheimer’s disease has shown that lipid rafts are involved in protein regulation and trafficking.5 The complexity of membranes associated with live cells makes it difficult to acquire meaningful information about these domains.

Model systems however, such as those fabricated using the Langmuir-Blodgett (LB) technique, are useful in decreasing the complexity by creating well defined, reproducible membrane mimics.6

Recent experiments have utilized time-of-flight secondary ion mass spectrometry

(TOF-SIMS) to examine LB films, lipid interactions and the process of domain formation in cellular membranes.7-11 These studies utilize the chemical imaging ability and the high surface sensitivity of TOF-SIMS to show it is an excellent tool to examine model membrane systems. So far, the work conducted with TOF-SIMS and LB model membrane systems has been largely limited to films containing phospholipids (such as dipalmitoylphosphatidylethanolamine (DPPE), dipalmitoylphosphatidylcholine (DPPC) and sphingomyelin (SM) and cholesterol). An important step for the building of simple but more representative biological membranes is to insert purified integral membrane proteins into well-defined lipid model membranes.12 In one recent experiment, a ternary

LB monolayer film consisting of DPPC, dipalmitoylphosphatidylglycerol (DPPG) and

36 surfactant protein B (SP-B) has been examined by TOF-SIMS to determine the lipidic interaction partner of SP-B.13 This mammalian pulmonary surfactant is a complex lipid/protein mixture secreted by alveolar epithelial cells. The results show that the lipid partner of SP-B to be DPPC rather than the generally accepted DPPG. The mammalian pulmonary surfactant study reveals an unexpected result that is in conflict with other experimental data and is yet to be resolved.

To establish that lipid/protein interactions can be highly specific, here we utilize the integral membrane protein, glycophorin A (GpA), to determine whether the probability of domain formation depends upon the nature of the surrounding lipid. Model membrane systems consisting of phospholipids, cholesterol and GpA are constructed to imitate the inner and outer leaflets of a cellular membrane. A well-studied example is the cell membrane of the human erythrocyte (red blood cell), which consists of 43.6 % total lipids (32.5% phospholipid, 11.1% cholesterol), 49.2% proteins and 7.2% carbohydrates in weight percents.14 The inner leaflet of the human erythrocyte membrane contains mainly phosphatidylethanolamine (PE) and the outer leaflet contains mainly phosphatidylcholine (PC) and SM.15 The DPPC lipid combined with cholesterol and

GpA are used to represent the outer leaflet and DPPE combined with cholesterol and

GpA are used to represent the inner leaflet. The components of the films are combined in the same ratios as in the erythrocyte membrane. The results show that the

DPPC/cholesterol/GpA LB films exhibit a single homogenous phase, in accord with the fluid mosaic model, whereas the DPPE/cholesterol/GpA LB film exhibits heterogeneity and domains within the LB film.

37 The reliability of the measurements has been considerably enhanced by establishing the influences of lipid mixtures on the SIMS secondary ion yield and by utilizing principal component analysis (PCA) to enhance the contrast of the images. In general, our results suggest that the presence of integral membrane proteins can exert both lateral and longitudinal regionalizations within the construct of the model membrane mimics.

3.2 Experimental Section

3.2.1 Materials

DPPC, DPPE, cholesterol (Avanti Polar Lipids, AL, USA) GpA, 16- mercaptohexanoic acid, methanol and chloroform (Sigma-Aldrich, MO, USA) were obtained and used without further purification. Water used in production of all LB films was purified by a Nanopure Diamond Life Science Ultrapure Water system (Barnstead

International, Dubuque, IA).

3.2.2 LB film construction

Single crystal (1 0 0) 3 inch wafers were cut and piranha etched (3:1 H2SO4:H2O2) before further treatment. A layer of 100 Å of Cr followed by 2000 Å of Au was then deposited onto clean silicon as described previously.16 A solution of 1mM 16– mercaptohexanoic acid in propan-2-ol was used to form self-assembled monolayers on gold.

38 The LB films were prepared using a Kibron µ Trough S-LB (Helsinki, Finland) with an aqueous sub-phase of 70 ml Mili-Q purified room temperature water. The final resistivity of the water was 18.2 MΩ with a total organic content of less than 5 ppb. All lipid and protein mixtures were dissolved in a 9:1 chloroform/methanol solution. After application the film was exposed to air for 20 minutes to ensure complete solvent evaporation. Trough barriers were computer controlled to allow uniform compression and constant feedback when depositing monolayers. Surface pressure–area isotherms were obtained. Films were deposited vertically onto a SAM substrate at 5 mN m-1 and the pulling rate was 3 mm min-1.

In this model system, the phospholipid content of the LB films is represented by one phospholipid (DPPC for the outer leaflet and DPPE for the inner leaflet) and the protein content is represented by the single integral membrane protein GpA. The LB films were prepared not only as reference materials for future study but also to imitate the inner and outer leaflets of the cellular membrane. Five films were prepared;

DPPC/cholesterol; DPPE/cholesterol; GpA; DPPC/cholesterol/GpA and

DPPE/cholesterol/GpA. The components of DPPE/cholesterol/GpA and

DPPC/cholesterol/GpA were combined in the correct ratio to imitate the erythrocyte membrane. This procedure results in the synthesis of a film imitating the outer leaflet with a molar ratio of DPPC 60% : Cholesterol 38% : GpA 2% and a film imitating the inner leaflet with a molar ratio DPPE 65% : Cholesterol 33% : GpA 2%. The surface pressure-area isotherms for these two films are shown in Figure 3-1 . The surface pressure area isotherms for the single components (not shown) match those reported earlier.6,7 These plots confirm the purity and concentration of the solutions used to make

39 the films. The phase changing point for the DPPE ternary film is ~ 52 Å2 and for the

DPPC ternary film is ~ 57 Å2, and is found to be reproducible to less than 1 Å.

Figure 3-1: Surface pressure – area isotherms for inner and outer membrane leaflet LB mimics. The outer leaflet plot is displaced upward by ∼ 0.5 nN m-1 for purposes of visual clarity.

3.2.3 Sample preparation for matrix effect study

Cholesterol, DPPE, DPPC and GpA were obtained from Sigma-Aldrich and used without further purification. Solutions in chloroform were prepared in the 3 component

LB films (DPPE 65%: Cholesterol 33%: GpA 2% and DPPC 60%: Cholesterol 38%:

GpA 2%). The SIMS information was obtained from the single components as well as the mixed component films. Sample preparation consists of pipetting 5 µl of each solution was onto a silicon wafer by spin casting for 30 s to ensure uniform solvent evaporation.

40 3.2.4 TOF-SIMS analysis

The mass spectral imaging was carried out on a specially constructed SIMS instrument described elsewhere.17 Analysis was performed with a 20-keV Ga+ primary ion beam system (Ionoptika Ltd, UK). Secondary ions were analyzed in a two-stage reflectron mass spectrometer (Kore Technology Ltd, U.K.). The primary ion dose density did not exceed 1 × 1012 ions cm-2. The ternary mixtures for the matrix effect experiments were analyzed with a 20-keV Au+ primary ion beam system. No evidence for sample charging was observed in any of these experiments.

3.2.5 Data analysis

Initial image processing was performed using specially constructed software.

Principal component analysis was performed using software written using Matlab™.

Principal component analysis is an unsupervised technique which is used to reduce the number of variables used to represent a complex data set with minimal loss of information, to identify relationships between variables and to identify relationships between samples. In the case of SIMS image analysis, the ion peaks are considered as variables and the image pixels as samples.18 A comprehensive review and explanation of the imaging PCA technique has been published recently.19

41 3.3 Results and Discussion

The goal of this study was to investigate lateral and transverse regionalizations of an integral membrane protein in the cell membrane. To study this we utilize inner and outer membrane mimics based upon the asymmetry of phospholipids in the cell membrane. Reference LB films of each component were analyzed to identify diagnostic fragment ions and to verify our results the matrix effect inherent to the systems under analysis was qualified. Once this has been achieved the measurements on the inner and outer membrane leaflets were analyzed and any resulting domains verified in light of the matrix effect results. PCA was then performed on the mass spectral images to increase the contrast of the images and refine the peak assignments associated with the domains.

3.3.1 Reference LB films of lipids

To establish expected secondary ion intensities and to determine any interaction between the components that might lead to artifacts, a series of control films consisting of lipid and cholesterol were examined in detail as summarized in Table 3-1 . The representative peaks chosen are consistent with those used in earlier studies.20,21 In this study the fatty acid tail group at m/z 551.50 and PE headgroup at m/z 142.03 is utilized to identify the presence of DPPE in the inner leaflet mimic. The PC headgroup at m/z

184.07 identifies DPPC in the outer leaflet mimic and m/z 369.35 is utilized to monitor the distribution of cholesterol.

Table 3-1: Diagnostic fragment ions from cholesterol, DPPC and DPPE that are present in DPPC / cholesterol and DPPE / cholesterol films. Parent Molecule Fragment m/z + DPPE & DPPC Dipalmitoyl – [C35H67O4] 551.50 + DPPE & DPPC Palmitoyl - [C19H37O3] 313.27 Cholesterol Cholesterol - [M-OH]+ 369.35 Cholesterol Cholesterol – [M-H]+ 385.35 + DPPC Phosphocholine Headgroup - [C8H19NPO4] 224.11 + DPPC Phosphocholine Headgroup – [C5H15NPO4] 184.07 + DPPC Phosphocholine Headgroup - [C5H13NPO3] 166.06 + DPPC Phosphocholine Headgroup - [C5H14NO] 104.11 + DPPC Phosphocholine Headgroup - [C5H12N] 86.10 DPPC DPPC – [M+H]+ 734.56 + DPPE Phosphoethanolamine Headgroup - [C2H9NPO4] 142.03 + DPPE Phosphoethanolamine Headgroup - [C2H7NPO3] 124.02

Proteins are observable in TOF-SIMS spectra through the presence of immonium ions from their constituent amino acids. GpA is mainly composed of glutamic acid (Glu), isoleucine (Ile), proline (Pro), serine (Ser), threonine (Thr) and valine (Val). These 6 amino acids make up 57.9 % of the composition. GpA contains no cysteine (Cys) or tryptophan (Trp). These 6 amino acids with their protonated molecular weights and common SIMS mass spectral ions are shown in Table 3-2 . The TOF-SIMS spectra of the positive ions of GpA, DPPE / cholesterol and DPPC / cholesterol LB films with SIMS peaks attributable to their components (Table 3-1 and 3-2) are shown in Figure 3-2 .

Table 3-2: Amino acid molecular weights and common mass spectral ions compiled from references [22,23,24]. Formulas are shown where given. Amino Acid [M+H]+ Mass spectral ions (m/z) + + Glutamic Acid 148.13 70, 84 [C4H6NO] , 102 [C4H8NO2] , 130, 148, (Glu) 175, + Isoleucine (Ile) 132.17 56, 58, 69, 86 [C5H12N] , 132, 263 + + Proline (Pro) 116.13 68 [C4H6N] , 70 [C4H8N] , 116, 117, 138, 231 + + Serine (Ser) 106.09 57, 60 [C2H6NO] , 71 [C3H3O2] , 91, 116, 106, 128 + + Threonine (Thr) 120.12 56, 57, 69 [C4H5O] , 74 [C3H8NO] , 116, 120, 239 + + Valine (Val) 118.15 55, 57, 59, 72 [C4H10N] 83 [C5H7O] , 118, 235

18000 A 20000 16000

18000 14000 m/z 45 16000 12000 10000 m/z 55 14000 m/z 70 8000 m/z 57 12000 Intensity m/z 86 6000 10000 m/z 74 m/z 89 4000 m/z 59 m/z 144 Intensity 8000 2000

6000 0 40 60 80 100 120 140 4000 m/z 2000

0 0 200 400 600 800 1000 m/z B 17500 m/z 369 40 0 1000 m/z 551.5 800 15000 m/z 385 600 20 0 Intensity Intensity 400 12500 200 0 0 360 3 65 37 0 37 5 380 3 85 39 0 550 .0 550 .5 5 51.0 5 51.5 55 2.0 552 .5 553.0 10000 m/z m/z

Intensity 10 00 7500 800 m/z 124 600 m/z 14 2

5000 Intensity 400 200 2500 0 120 125 130 135 140 145 m/z 0 0 200 400 600 800 1000 200 m/z m/z 734 14000 C 100

12000 Intensity

10000 0 730 735 740 8000 800 m/z 700 m/z 184 600 m/z 369

Intensity 6000 500 400 m/z 385

4000 Intensity 300 200 2000 100 0 360 380 m/z 0 0 200 400 600 800 1000 m/z

45 3.3.2 Evaluation of possible matrix effect

Previous studies have suggested that secondary ion yields strongly depend upon the chemical composition of the lipid film. For example it has been reported that the presence of PC suppresses the ion intensity of PE, presumably by gas phase exchange processes [21]. To test for these effects TOF-SIMS spectra were obtained from the pure solutions of DPPC, DPPE, cholesterol and GpA. Secondary ion intensities of diagnostic fragment ions were determined and converted into an effective secondary ion yield by normalizing to the incident beam current. The headgroup fragment m/z 184 was used to identify DPPC, m/z 369 to identify cholesterol and headgroup fragment m/z 142 to identify DPPE. To identify GpA the sum of m/z 45, 59, 72, 89 and 144 was utilized since reference and library spectra indicate these peaks are not present to any significant extent in the spectra of the lipids and cholesterol. Secondary ion yields obtained from the pure compounds and the secondary ion yields expected for the ternary mixtures based upon molar ratio percentage are shown in Table 3-3 . These numbers shall be compared with the measured values, also shown in Table 3-3.

Table 3-3: Secondary ion yields from pure films, expected secondary ion yield for the DPPC and DPPE ternary mixtures and measured secondary ion yields for the DPPC and DPPE ternary mixtures. 1Yield is determined as the number of secondary ions per incident primary ion. 2 Percentages represent the molar percent of each component in the ternary film. Ion m/z Yield1 of Expected Expected Measured Measured (original) Pure yield yield DPPE yield yield DPPE Compound DPPC ternary DPPC ternary ternary mixtures ternary mixture mixture mixture 184 (DPPC) 1.41 × 10 -4 8.46 × 10-5 1.30 × 10-4 (60 %)2 142 (DPPE) 3.84 × 10-6 2.50 × 10-6 3.84 × 10-6 (65 %) 369 4.91 × 10-6 1.87 × 10-5 1.62 × 10-6 3.98 × 10-6 3.22 × 10-6 (Cholesterol) (38 %) (33 %) Amino Acid sum 4.70 × 10-5 9.40 × 10-7 9.40 × 10-7 3.84 × 10-5 6.43 × 10-5 (GpA) (2 %) (2 %)

The expected secondary ion yields (blue) and the measured secondary ion yields for the DPPC and DPPE ternary mixtures are displayed in Figure 3-3 . For the DPPC ternary mixture there is a relative yield enhancement of GpA and a relative yield suppression of cholesterol when comparing the measured yield observed in the ternary mixture to the calculated yield. These results show that detection of lipid and protein signals is possible when the compounds are present in a chemical environment that contains both of them. Moreover, significant cholesterol signal is still visible in the ternary mixture

(a) 14 )

-5 Measured yield 12 Calculated yield

Secondary Ion Yield (x 10 Ion Yield (x Secondary 0 DPPC Chol GpA

(b)

) 7 -5 Measured Yield 6 Calculated Yield 5

Secondary Ion Yield (x 10 Ion Yield (x Secondary 0 DPPE Chol GpA Figure 3-3: (a) The expected secondary ion yield for DPPC, cholesterol and GpA based upon pure yield and molar ratio (green) and the measured yield observed from the DPPC ternary mixture (blue). (b) The expected secondary ion yield for DPPE, cholesterol and GpA based upon pure yield and molar ratio (green) and the measured yield observed from the DPPE ternary mixture (blue)

For the DPPE ternary mixture there is a relative yield enhancement of GpA compared to a relative yield suppression of DPPE and cholesterol. These results show that if domains of DPPE and cholesterol are present on the DPPE/cholesterol/GpA film

48 and GpA is present in these areas it would be preferentially observed over cholesterol and

DPPE. Hence in domains that are rich in protein it is possible to have small quantities of

DPPE, cholesterol or both in these areas which might not be detected due to the suppressing effect of GpA.

3.3.3 GpA reference LB film

Mass spectral images of the GpA film are shown in Figure 3-4 . The images depict a single homogenous phase for GpA based upon diagnostic fragment ions attributable to valine, arginine and glutamic acid. Images from this reference film illustrates that it is possible to construct an LB film from GpA and detect amino acid fragments from the film.

400 µm 400 µm

Total Ion m/z 59 m/z 72 m/z 102 Figure 3-4: Mass spectral images of GpA LB film

3.3.4 Outer membrane leaflet mimic LB film (DPPC/cholesterol/GpA)

With mass spectra and matrix effects of each component known, it is feasible to acquire TOF-SIMS images of the synthesised membrane mimics. Images from the

49 DPPC/cholesterol/GpA LB film for each characteristic mass are shown in Figure 3-5 .

No domain formation is observable from the total ion image. The peaks from the phospholipid component at m/z 184.07, the cholesterol component at m/z 369.35 and valine/arginine related ions from GpA components at m/z 59.07 and m/z 72.08 are also uniform in coverage. The overlay image represents peaks from all three components in their respective colours summed to represent lateral distribution. From all of these representations the DPPC/cholesterol/GpA LB film appears to form a single homogenous phase on the scale observable by TOF-SIMS. The homogeneity of the films has been confirmed with repeat measurements.

400 µm 400 µm

Total Ion m/z 184 m/z 369 m/z 59

m/z 72 Overlay m/z 184,369 and 59

Figure 3-5: Mass spectral images of DPPC/cholesterol/GpA LB film with m/z 184 representing DPPC, m/z369 representing cholesterol, and m/z 59 and m/z 72 representing GpA.

50 3.3.5 Inner membrane leaflet mimic LB film (DPPE/Cholesterol/GpA)

The TOF-SIMS images of the inner leaflet mimic are shown in Figure 3-6 and

Figure 3-7 . The distribution of the dipalmitoyl tailgroup peak at m/z 551.5 exhibits clear heterogeneity. Moreover, the PE fragments at m/z 142.03 (not shown) and m/z 124.02

(not shown) and the cholesterol peaks at m/z 369.35 and m/z 385.35 (not shown) exhibit an identical pattern. This information suggests there is a co-localization of DPPE and cholesterol, with voids of signal throughout the image that are not occupied by these species. The mass spectral images of the DPPE, cholesterol and GpA LB film which can be attributed to SIMS peaks m/z 59 (valine / arginine), m/z 70 (arginine / glutamic acid / leucine / proline), m/z 71 (serine), m/z 72 (valine), m/z 84 (glutamic acid, glutamine, lysine) and m/z 102 (glutamic acid) are shown in Figure 3-7. These ions are respresentative of protein fragments as noted in Table 3-2 and Figure 3-2. The images show that only some of the amino acid peaks selected from the known composition of

GpA show heterogeneity throughout the film. This apparent difference arises from the presence of significant chemical background noise in this low mass range. For example m/z 59, m/z 70, m/z 71, m/z 72, m/z 84 and m/z 102 are all observable in the DPPE and cholesterol LB film with m/z 70, m/z 71 and m/z 84 the most prominent.

400 µm 400 µm

Total Ion m/z 551.5 m/z 369

Figure 3-6: Mass spectral images of the DPPE/cholesterol/GpA LB film with m/z 551 representing DPPE and m/z 369 representing cholesterol.

400 µm 400 µm

m/z 59 m/z 70 m/z 71

m/z 72 m/z 84 m/z 102

Figure 3-7: Mass spectral images of the DPPE / cholesterol / GpA LB film showing peaks attributable to amino acids

52 The three components of the DPPE, cholesterol and GpA film are clearly visible in Figures 3-6 and 3-7. The mass spectral images show that DPPE and cholesterol are co-located and anti-correlated to areas of high protein. The heterogeneity reveals that the inner membrane LB film contains two separate phases; a GpA phase and a DPPE and cholesterol phase on the scale observable by TOF-SIMS. The heterogeneity of the films has been confirmed by repeat measurements. However, some of the spectral images attributed to amino acid fragments exhibit signal originating from the entire image. This observation could point to the presence of a third phase of DPPE / cholesterol / GpA or could arise from the fact that the low molecular mass fragments may originate from sources other than protein.

3.3.6 Principal component analysis

To refine these assignments PCA is employed to determine which peaks distinguish these domains and to increase the contrast of the images. This analysis was performed on the two total ion images previously shown in Figure 3-5 and Figure 3-6.

The mass range of 1-1000 Da was utilized to include the major peaks from all three components of the LB films. The scores plot for principal component 1 of the SIMS total ion image for the DPPE/cholesterol/GpA LB film in Figure 3-6 is shown in Figure 3-8 .

Figure 3-8: Principal component 1 scores plot for the DPPE / cholesterol / GpA. The total ion image associated with this data is shown in Figure 6.

Each principal component score has an associated loading which shows the SIMS peaks responsible for the discrimination observed in the image. The loadings, as shown in Figure 3-9 , have a positive and negative direction on the y axis. The peaks observable in these directions correspond to the color scale at the side of the image. If there is a high concentration of peaks in the positive direction of the y axis this area in the image is observed as red. If there is a high concentration of peaks in the negative direction of the y axis in the image this area is observed as blue. This method allows visualization of the areas of the film with different surface chemistry and provides mass spectral information about the discrimination.

Loading on principal component 1 Loading on principal component 1 1.21.2 1.21.2 AB 11 (a)11 (b) m/z 45 0.80.8 0.80.8

0.60.6 0.60.6 m/z 72 0.40.4 0.40.4 m/z 59 m/z 89 m/z 144 0.20.2 0.20.2 Loading on on Loading principalcomponent 1 on Loading principalcomponent 1 00 00

-0.2 -0.2 -0.2 100 200 300 400 500 600 700 800 900 1000 -0.2 20 40 60 80 100 120 140 160 180 200 Loading on principal component1 100 200 300 400 500 600 700 800 900 1000 Loading on principal component1 20 40 60 80 100 120 140 160 180 200 m/zm/z m/z -3 Loading on principal component 1 x 10 Loading on principal component 1 0.0050.005 1 1 CD(c) (d) 0 0 0 0 -1-1 -0.005-0.005 -2-2 -0.01-0.01 -3-3 -0.015-0.015 m/z 385 -4-4 Loading on on Loading 1 principalcomponent Loading on on Loading principal 1 component -0.02 -0.02 -5-5 m/z 552 m/z 369 -0.025-0.025 -6 360 365 370 375 380 385 390 395 400 545 550 555 560 Loading on principal component1 Loading onprincipal component1 360 365 370 375 380 385 390 395 400 -6545 550 555 560 m/z m/z Figure 3-9: Loading plots for principal component 1 (a) m/z 1 – 1000, (b) m/z 0 – 200, (c) m/z 360 – 400 and, (d) m/z 545 – 560.

During PCA, the spectra of the images are binned to nominal mass (1 amu) to ease computational demands. This means that the dipalmitoyl tailgroup peak at m/z

551.5 appears at m/z 552 in the loadings, as seen in Figure 3-9(d). This identification of has been verified as the dipalmitoyl tailgroup peak at m/z 551.5 from the original data.

The peaks in the positive direction are responsible for the red area on the principal component 1 scores image. The peaks originate from DPPE (m/z 552), cholesterol (m/z

369 and 385) and contributions from low molecular mass fragments that can be attributed to hydrocarbons. The loadings in the negative direction are attributed to GpA as m/z 59 and 72 are both attributed to valine. The m/z 45 peak [HOCO]+ is a fragment ion that can

55 be attributed to the carboxy terminus of the amino acids [25], m/z 89

+ [NH2CH3CHCOOH] is a fragment ion attributable to alanine [25] and m/z 144

+ [CH3CONHCHCH2CH2CH2COOH] has been attributed to a fragment ion of the tripeptide (OMe)-Ala-Leu-OM.26 These mass spectral ions appear in the original data for the GpA LB film and localize to the same area of the image as the identified amino acid peaks in the DPPE, cholesterol and GpA LB film. Mass spectral images of m/z 45, m/z

89 and m/z 144 for the DPPE ternary film is shown in Figure 3-10 , while m/z 59 and m/z

72 are shown in Figure 3-7. Hence, the mass spectral ions identified by PCA as the protein components preferentially locate to the protein domain (Figures 3-10 and 3-7) and ions identified as lipid / cholesterol components domain preferentially locate to the lipid / cholesterol domain (Figure 3-6).

m/z 45 m/z 89 m/z 144

Figure 3-10: Mass spectral images of m/z 45, m/z 89 and m/z 144 for the DPPE/cholesterol/GpA LB film.

It is interesting to compare the PCA scores of the heterogeneous DPPE ternary film to the more uniform DPPC ternary film. The scores plot for principal component 1 of the SIMS total ion image for the DPPC/cholesterol/GpA LB film in Figure 3-5 is

56 shown in Figure 3-11 and the loadings plots for principal component 1 is shown in

Figure 3-12 . These plots reveal that any observed heterogeneity arises from a polydimethylsiloxane (m/z 73 and m/z 147) surface contaminant. The scores image shows no evidence for any distinct protein domains. The PCA analysis of the

DPPC/cholesterol/GpA LB film supports the conclusion drawn from the original SIMS data that the DPPC/cholesterol/GpA LB film exists as a single phase.

Figure 3-11: Principal component 1 scores plot for the DPPC/cholesterol/GpA total ion image shown in Figure 3-4(b).

0.6 0.25 1

0.5 (a) 0.2 (b)

0.4 0.15

0.3 0.1 Component

0.2 0.05

0.1 0 Principal

on 0 -0.05

-0.1 -0.1 Loading -0.2 -0.15 100 200 300 400 500 600 700 800 900 1000 50 60 70 80 90 100 110 120 130 140 150

m/z m/z Figure 3-12: Loading plots of principal component 1 for the DPPC/cholesterol/GpA: (a) m/z 1-1000, (b) m/z 50-150.

3.4 Conclusions

The LB film outer leaflet membrane mimic shows the existence of a single homogenous phase across the DPPC/cholesterol/GpA LB film and the inner membrane leaflet displays two phases, a DPPE/cholesterol phase and a GpA phase. These results suggest there is a transverse regionalization of GpA between the inner and outer leaflet of a cell membrane. This behavior is in contrast to the fluid mosaic model whereby all lipid and protein molecules are suggested to diffuse more or less freely in the cell membrane.

Qualitative analysis of the precise chemical composition of the observed domains is complicated by the presence of matrix effects. The homogeneity observed when analyzing the DPPC/cholesterol/GpA LB film is supported by the matrix effect results on the same system as the matrix effect results show that the detection of lipid and protein signals is possible when they are combined together in a chemical environment and if the

58 DPPC ternary film did contain protein domains, the matrix effect results show that it would be possible to detect these domains by the SIMS technique. The heterogeneity observed when analyzing the DPPE/cholesterol/GpA is supported by the matrix effect results on the same system by verifying that the detection of protein domains is possible.

However as GpA suppresses DPPE and cholesterol it is possible to have to have small quantities of these components within a protein domain.

These two monolayer films differ only by the chemical nature of the phospholipid headgroup, yet the distribution of membrane protein is dramatically different. The choline headgroup consist of an –N(CH3)3, while the ethanolamine terminates with a –

NH3 group. We speculate that this different chemistry allows strong DPPE-DPPE hydrogen bonding interactions that encourage tight structural integrity, opening the possibility of protein exclusion.5 The phosphocholine molecules do not exhibit this attraction and are free to mix with the various components in the film. At this point, it is unclear whether these same factors drive asymmetry in a real biological membrane since much more complex chemistry is involved. For example, recent studies of a ternary mixture of cholesterol, SM and palmitoyloleoylphosphatidylcholine (POPC) show that the degree of tailgroup saturation is important in determining the composition and degree of domain formation.20 TOF-SIMS has been shown as a sensitive technique for the analysis of lateral and longitudinal regionalizations in cell membrane mimics. In this investigation we have demonstrated that such sensitivity can be utilized to identify a transverse regionalization of an integral membrane protein that is dependent upon phospholipid composition of the membrane mimic.

59 3.5 Acknowledgements

The authors would like to acknowledge the World University Network and the

EPSRC for funding to carry out this research and Dr. Alex Henderson for his help and expertise on the multivariate image analysis. Financial support from the National

Institute of Health under grant #EB002016-13 and the National Science Foundation under grant #CHE-555314 are also acknowledged.

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Chapter 4

Chemically Alternating Langmuir-Blodgett Multilayer Films as a Model for Molecular Depth Profiling

This chapter has been reproduced with permission from L. Zheng, A. Wucher, and N. Winograd, “Chemically Alternating Langmuir-Blodgett Thin Films as a Model for

Molecular Depth Profiling by Mass Spectrometry”, Journal of the American Society for

Spectrometry.

4.1 Introduction

Polyatomic projectiles have expanded potential applications of secondary ion mass spectrometry (SIMS) experiments 1-3. An important modality is to obtain molecular information as a function of depth via mass spectrometry using the polyatomic ion-beam to erode through organic and/or biological samples 4-8. Molecular depth profiling of this type has generally not been possible with traditional atomic projectiles due to accumulation of ion-induced damage accumulation 9;10. For bombardment with molecular clusters, however, the chemical damage is often removed as fast as it accumulates, leaving the sample underneath relatively intact 11;12. Ultimately, 3 dimensional mass spectral analysis of complex molecular systems can be achieved with the combination of molecular depth profiling and SIMS imaging 13;14. Although several different projectiles have been shown to be effective for these types of experiments, we

63 4;7;8;15 + and others have reported that buckminsterfullerene (C60 ) is particularly effective in this regard.

With the emergence of cluster SIMS, a fundamental understanding of the sputtering process is needed to optimize the parameters for molecular depth profiling. An essential element for experimental investigation of the interaction between energetic cluster ions and a molecular solid is the availability of a model system which has a well- defined chemical structure and can be reproducibly synthesized. Previously, we have utilized 300-nm trehalose sugar films spin-cast onto Si substrates as such a platform 8;11.

Recently, Shard et.al. has reported on a different system consisting of organic delta layers and demonstrates the depth dependence of depth resolution 16. Together with an analytical model, parameters such as depth resolution, sputtering yield and the thickness of the altered layer at the surface were able to be estimated.

Earlier experiments have suggested that multilayer films prepared by Langmuir-

Blodgett (LB) techniques might make a good model for more complicated systems 11;12.

Here we show how this technology can be employed to construct samples consisting of multilayers of organic thin films with varying chemical composition. The specific goals of this preliminary study are to establish the degree of ion-beam induced chemical damage that occurs during depth profiling and to determine the degree of mixing that occurs between the layers during erosion. Ultimately, we hope that this platform will allow optimization of the parameters necessary to characterize buried interfaces using cluster SIMS.

Langmuir-Blodgett (LB) films are formed by amphiphilic molecules at the air- water interface and are subsequently transferred to a solid substrate to form monolayers

64 and multilayers 17-19. By changing the type of molecule applied to the air-water interface, it is straightforward to form layers with differing chemical composition. More importantly, LB multilayers have been well-characterized and are known to form sharp boundaries between the layers due to the amphiphilic character of the molecules 18-25. In this study, LB films of barium arachidate and barium dimyristoyl phosphatidate

+ alternating in varying thicknesses are formed and depth profiled by a 40-keV C60 ion beam. The morphology of the surfaces before, during and after bombardment is monitored using atomic force microscopy (AFM). The results show that the profile of molecular-specific ion signals accurately represents the chemical structures of these LB films through at least 300 nm of erosion. The extent of how well these structures are resolved by depth profiling suggests that the depth resolution is on the order of 20 nm. In general, we suggest that this system is well-suited as a model to fully investigate the experimental parameters necessary for optimization of molecular depth profiling experiments.

4.2 Experimental Section

4.2.1 Materials

Arachidic acid (AA), barium chloride (99.999%), potassium hydrogen carbonate

(99.7%), and copper(II) chloride (99.999%) and solvents were purchased from Sigma-

Aldrich (Allentown, PA). Dimyristoyl phosphatidic acid (DMPA) was purchased from

Avanti Polar Lipids (Alabaster, AL). All the chemicals were used without further

65 purification. The high purity water used in preparation of all LB films was obtained from a Nanopure Diamond Life Science Ultrapure Water Systems (Barnstead International,

Dubuque, IA) and has a resistivity of 18.2 MΩ-cm.

4.2.2 Substrate and LB film preparation

Single crystal (100) silicon wafers 3 x 3 inches square were employed as the substrate for all the films. The Si substrates were cleaned by submerging the substrates in a piranha etch solution (3:1 H2SO4/H2O2) for 10-15 minutes and rinsed with high purity water several times to ensure the hydrophilicity of the Si/SiO2 surface. (Extreme caution must be exercised when using piranha etch. An explosion-proof hood should be used.) A

Kibron μTrough S-LB (Helsinki, Finland) was used for isotherm acquisition and multilayer LB film preparation. The subphase contained 70 mL of aqueous solution of

-4 -3 -7 10 M BaCl2, 10 M KHCO3, and 10 M CuCl2. The BaCl2 was added to form salt with arachidic acid and DMPA at pH 7 which was adjusted by addition of KHCO3. The CuCl2 was used to enhance film stability after synthesis of a large number of layers.

Monolayers of AA and DMPA at the air-water interface were aged for 30 min and compressed at a constant rate of 7 Å2/molecule /min. When the surface pressure reached

33 mN/m, the film was transferred onto the Si substrate by vertical deposition at the rate of 10 mm/min. The surface pressure was measured and kept constant during film transfer by a Wilhelmy wire interfaced to a personal computer. At least 3 layers of AA were always applied onto the substrate initially to ensure further multilayer formation. An

66 even number of DMPA or AA layers were deposited consecutively. The films were allowed to dry for 15 minutes between each deposition.

4.2.3 Instrumentation

Depth profiling of LB films was performed by a TOF-SIMS instrument described

5 + previously . The system is equipped with a 40-keV C60 ion source (Ionoptika;

Southampton, U.K.), which is directed to the target at an angle of 40º relative to the

+ surface normal. Under typical operating conditions, the C60 ion source delivers a 0.2 nA ion current at a 30 µm probe size onto the analysis stage. The samples were sputtered

+ over an area of 200 µm x 300 µm in dc mode by the C60 ion beam during depth profiling.

The erosion time of each cycle varies from 3 to 10 sec. Between erosion cycles, SIMS spectra were taken from a smaller area of 50 µm x 75 µm located at the center of

+ 10 -2 sputtered region. The C60 fluence was kept below of 10 cm to avoid any possible effects of beam induced damage during spectral acquisition. The mass spectrometer was operated in a delayed extraction mode with 50 nsec delay time between the primary ion pulse and the secondary ion extraction pulse. Charge compensation was found to be unnecessary for positive SIMS mode. Secondary ion intensity was calculated by integrating the peak area of the corresponding mass value. Mass resolution of ~2500 was achieved at m/z 500. All depth profiles were recorded after cooling the substrate to 100

K. Cooling was necessary to avoid thermally-induced mixing of the layers, and yielded results with considerable improved depth resolution.

67 4.2.4 Ellipsometry and AFM measurements

The crater depth was measured by AFM (Nanopics 2100, KLA-Tencor, San Jose,

CA) with a maximum field of view of 800 µm x 800 µm in contact mode. The thickness of the LB films was determined by a single-wavelength (632.8 nm, 1 mm spot size, 70° angle of incidence) Stokes ellipsometer (Gaertner Scientific Corporation, Skokie, IL; model LSE) and the value is averaged over at least three measurements.

4.3 Results and Discussions

Using LB technology, our strategy is to construct a series of multilayer thin films whose thickness varies from a few nanometers to about 50 nm in order to assess the ability of cluster SIMS to distinguish between the layers. LB films have well-defined interfaces and exhibit very little chemical mixing between each layer,19 which make it suited for fundamental studies of cluster ion induced interface mixing and depth resolution. This work is focused on developing LB multilayers as a stable and robust platform so that more fundamental issues of molecular depth profiling can be understood.

4.3.1 LB film characteristics

LB multilayers are prepared using layer-by-layer deposition on clean Si substrates.

The resulting films are stable under ambient condition for over 1 month as indicated by their color, mass spectra and depth profiles. The barium ions in the subphase form barium salts with AA or DMPA under pH 8 which is controlled by KHCO3. This pH

68 value allows monolayers to be transferred smoothly onto the substrate with a minimum of defects.24 The monolayers are transferred at a surface pressure of 33 mN/m, a pressure corresponding to the solid phase region. At that surface pressure, each AA and DMPA molecule occupies an area of 20 Å2 and 41 Å2, respectively. These molecular areas lead to a corresponding monolayer density of 5.0 x 1014 molecules/cm2 and 2.5 x 1014 molecules/cm2. These numbers can be used to accurately calculate the sputtering yield, defined as the number of molecule equivalents removed per incident particle.

Figure 4-1: Schematic drawing of 3 alternating Langmuir-Blodgett films with thickness of each block and number of layers listed.

The films are prepared by creating a block of AA multilayers, switching the monolayer on the subphase to DMPA, and preparing a block of DMPA multilayers on top of the AA block. This process is then repeated many times to produce films shown schematically in Figure 1. The thickness of each film equals the thickness of one monolayer multiplied by the number of layers applied to the substrate. The monolayer

69 thicknesses for AA and DMPA are 2.7 nm and 2.2 nm, respectively, as measured by 3-2 ellipsometry. The values of the thicknesses of each building block and of the entire film for the substrates examined in this work are noted in the Figure 3-1. The use of films with different block size will allow a test of the depth resolution during depth profiling as shown later.

The LB films have different colors depending upon thickness due to optical interference. A light microscope image of LB20 after depth profiling is shown in Figure

3-2(a). The exposed Si crater formed by C60 erosion is seen as a grey rectangle, while the blue area is the virgin LB film. The uniformity of the color is indicative of uniform film deposition.

In addition to light microscopy, AFM is also used to characterize the LB films, as illustrated in Figure 3-2(b). The crater is determined to be 200 µm x 300 µm and the crater depth is measured to be 330 nm for the LB20 sample. For this situation, the LB film itself is calculated to be 307 nm in thickness, as determined from the known number of layers deposited multiplied by the appropriate monolayer thickness as determined by ellipsometry. The difference between the numbers is largely due to the fact that the AFM data include a small contribution from erosion into the Si substrate. The estimated yield

+ 26 of Si under 40-keV C60 bombardment is about 200 Si atoms/C60 and the fluence applied to the bare Si to form this crater is about 7 x 1013 ions/cm2. Hence, about 30 nm of Si will be eroded away. These numbers show that there is excellent agreement between AFM measurements of the crater, and ellipsometry measurements on the respective monolayers, providing additional evidence for the high quality of these LB multilayer structures. Figure 4-2

(a)

(b)

Figure 4-2: (a) Optical image of LB20 film with a crater in the middle which is created + after C60 depth profiling (the crater is the grey area which is surrounded by blue uneroded area), (b) AFM measurements of LB20 films with a crater which is formed by + C60 depth profiling.

It is possible to acquire an approximate indication of the surface roughness associated with these films. The AFM measurements on the clean Si substrate after the piranha etch show that over an area of 20 µm by 20 µm, the rms roughness is about 15 nm. Before the piranha etch, the roughness is about 1 nm, showing that this treatment is responsible for the new surface properties. Measurements on the LB film before sputtering yield a surface roughness of 20 nm, which does not change significantly with

+ film thickness. The roughness of the LB film, after C60 bombardment and before

71 complete removal of the film, was also measured to range from 20-25 nm. Hence, the

LB film roughness data suggest that there is minimal topography formation during bombardment, and that the film retains a planar configuration to at least a precision of 15 nm.

4.3.2 Characterization of LB films by SIMS

Before depth profiling, the SIMS spectra of the LB monolayers of AA and DMPA are determined. The monolayers are prepared under the same conditions as the multilayers to ensure mass spectral uniformity. The mass spectra and chemical structure of AA and DMPA are shown in Figure 3-3. The barium containing peaks dominate both spectra and provide more specific chemical information 27. The characteristic peaks for

+ + AA are m/z 449 and m/z 463, corresponding to the [M-H+Ba] and [M-H+Ba+CH2] , respectively. Molecular ions for DMPA are not observed, however a high-mass fragment peak at m/z 525 is significant and unique to DMPA. Lower mass peaks at m/z 371 and m/z 355 are also characteristic of DMPA. Hence, for depth profiling, m/z 463 is used to represent AA and m/z 525 for DMPA.

(a) (b)

+ Figure 4-3: Chemical structures and C60 -induced mass spectrum of LB monolayer. (a) AA, and (b) DMPA. Both spectra have Ba+ at m/z 138 and BaOH+ at m/z 155. AA has characteristic peaks at m/z 463 and 471, while DMPA is characterized by peaks m/z 355, 371, and 525.

+ Depth profiles of the three LB films by C60 ion bombardment are displayed in Figure 4.

The integrated molecular-specific peak intensities of AA, DMPA, and Si, are plotted

+ + versus C60 ion fluence. Note that the SIMS peak at m/z 112 for the silicon cluster Si4 is

used instead of Si+ at m/z 28 due to the isobaric hydrocarbon interference. As shown in

Figure 3-4(a) for LB 20, the DMPA signal increases during the initial bombardment, then

reaches its maximum. The initial increase most likely arises from surface contamination

since it was not observed in the depth profile of fresh-made LB film. The signal remains

at a maximum value before decreasing as the AA signal begins to increase from baseline.

When the AA signal reaches its maximum, the DMPA signal reaches its minimum. This

73 completes the first cycle of the depth profile. Upon further bombardment, these cycles repeat themselves until the film/Si interface is reached. Note that the AA and DMPA maximum and minimum signal intensities remain nearly constant. The conservation of these molecular ion signals indicates that the ion bombardment does not create significant damage to the underneath layers, a result which is predicted by many molecular dynamics computer simulations of the bombardment process 10;28;29. In summary, the depth profile accurately represents the molecular structure of these alternating block LB films.

For LB12, where the block thickness is 26-32 nm, essentially the same profile is obtained as shown in Figure 3-4(b), except that the individual blocks are less well resolved. This trend is continued for LB6 in Figure 3-4(c), where the block thickness is

13-16 nm. This leads to a semi-quantitative estimation that the depth resolution should

+ range between 16 to 26 nm with the 40-keV C60 projectile.

Computer simulations of the ion bombardment of 20-keV C60 into a solid benzene matrix show that at normal incidence, a crater is formed at the surface with a depth of 4.2 nm, and a width of 8.7 nm [Postawa, Z. private communication]. As noted above, very little damage or mixing is observed below the crater. Hence, it is our view that the intrinsic limit to the depth resolution ought to be near the 4.2 nm value. The fact that our measured interface width is larger than this value could arise from a number of sources, including roughness of the Si substrate, angle of incidence of the projectile, thermal mixing even at reduced temperatures, and/or topography formation during erosion of the organic film. Figure 4-4

7000

6000

5000 ÷5 4000 AA 3000 DMPA 2000 Si

Signal (Counts) 1000

0 100 200 300 400 500 Fluence (C ions/cm2) 60

5000 (b) DMPA Si 4000 AA

3000

2000 ÷5

1000 Singal (Counts)

0 100 200 300 12 2 Fluence (x10 ions/cm )

6000 (c) Si 5000 AA DMPA 4000

3000 ÷5 2000

Signal (Counts) 1000

0 50 100 150 200 Fluence (x102ions/cm2) + Figure 4-4: C60 ion fluence dependence of AA, DMPA, and Si signals of (a) LB20, (b) LB12, and (c) LB6 films. AA, DMPA, and Si are represented by m/z 463, m/z 525, and m/z 112, repectively.

75 4.3.3 Calculation of depth resolution

It is possible to gain a semi-quantitative estimate of the interface width/depth resolution by examining the magnitude of the signal excursions in the depth profile, which has been explored for atomic depth profiling 30. These fluctuations can be described as a contrast as follows: Eq. 4.1

[Eq. 4.1]

where Smax and Smin are the maximum and minimum signal observed for one peak and SB is the residual background signal observed at the relevant m/z value. The SB value is determined from a two chemical block system consisting of films of sufficient thickness

(~140 nm) to allow steady state signals to be achieved. There is an intrinsic relationship between contrast and depth resolution. Assuming that the depth response function is the integral of the product of a delta function (representing the discrete layer interface) and a

Gaussian function, the depth resolution Δz equals 2σ, the half width of the Gaussian function. In the depth response function, Δz corresponds to the points where the signal drops from 84% to 16% intensity. If the chemical block, d, is much thicker than Δz, the signal coming from the chemical layer should reach a steady state and the contrast is unity. On the other hand, the contrast approaches zero when d is much smaller than Δz.

Between these 2 extreme situations, the contrast ranges from zero to one. The plot of contrast versus d/Δz is displayed in Figure 3-6 . Since the block thickness d is known for the LB films and the contrast can be measured from the depth profiles, the depth resolution is obtained by using this plot. The calculated depth resolution values of samples LB20 and LB12 are shown in Table 1, together with their measured contrasts.

76 The LB6 is not studied since the contrast is almost lost. Although d is different for the two samples, the calculated Δz values are similar for each interface and correspond well with our previous estimation. Hence, having access to a reproducible model system along with a simple strategy for measuring depth resolution provides a good starting point to quantify the molecular depth profile experiments. Figure 4-5

1.0

0.8

0.6

0.4 contrast 0.2

0.0

0.0 0.5 1.0 1.5 2.0 2.5 3.0

d / Δz Figure 4-5: The plot of contrast versus layer thickness (d) over interface width (Δz).

4.4 Conclusions

We have shown that it is possible to make alternating chemical structures with sharp interfaces by using LB techniques. These structures make excellent models for detailed characterization of the molecular depth profiles created using cluster SIMS. By utilizing the relationship between contrast and interface width, we have also calculated the depth resolution to be on the order of 17-35 nm, a value consistent with numbers

77 reported for polymer and organic/inorganic interfaces.7;8 Most importantly, the degree of interface mixing increases only slightly, at least up to a film thickness of 300 nm, as the multilayer structure is systematically removed. With this platform, it should be possible to examine the influence of a number of important properties on the quality of the depth profile. For example, we are looking for better ways to prepare an appropriate hydrophilic Si surface without having to employ the piranha etch, since this procedure adds some uncertainty to the depth scale via surface roughening. Other factors that can possibly affect the value of depth resolution are also under investigation, including bombarded area, projectile energy and projectile incident angle.

4.5 Acknowledgement

The material is based upon work supported by the National Institutes of Health under grant #EB002016-13, the National Science Foundation under grant #CHE-555314, and the Department of Energy grant # DE-FG02-06ER15803. We also thank Dr. David

Allara and his research group for the use of the ellipsometer, Dr. Thomas Mallouk and his group for the use of light microscopy.

4.6 References

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78 3. Jones, E. A.; Lockyer, N. P.; Vickerman, J. C. International Journal of Mass

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Chapter 5

Molecular Depth Profiling of Multilayer Langmuir-Blodgett Films to Investigate Optimal Depth Resolution

This chapter has been reproduced with permission from Zheng, L.; Wucher, A.;

5.1 Introduction

The development of polyatomic projectiles for cluster based secondary ion mass spectrometry (SIMS) is opening new opportunities for materials characterization. Of special interest is the emergence of molecular depth profiling whereby the projectile removes molecules in nearly a layer-by-layer fashion without the accumulation of chemical damage.1-7 This problem has plagued atomic projectiles for many years8 and has limited sensitivity. When the molecular samples are bombarded with cluster ion sources, the energy is deposited close to the surface and the chemical damage is then removed as fast as it accumulates, leaving sub-surface layers relatively intact.9-15 The quality of the depth profile has recently been characterized by a cleanup-efficiency parameter derived from a simple erosion model for molecular solids.16 Among all the

+ cluster projectiles, buckminsterfullerene (C60 ) generally exhibits the highest cleanup efficiency.17;18

81 New fundamental studies of the sputtering process are now required to optimize the experimental parameters for molecular depth profiling. The literature concerning the interactions between energetic cluster ions and molecular solids has grown rapidly, including experimental approaches19-26 and molecular dynamic (MD) simulations12;13;27-30.

While MD simulations have provided insightful understanding, much of the experimental work lacks a quantitative understanding for comparison to the simulation results.

Moreover, most of the molecular depth profiling experiments are performed on organic systems either with uniform chemical content or with unknown composition.3;4;31;32 The analysis of buried organic layers under cluster bombardment has been shown to be feasible but the degree of beam-induced mixing between organic layers is not fully understood. This information is important to cluster SIMS applications in biology since biomaterials are generally chemically heterogeneous and complex. Hence, it is essential to quantify the organic-organic interface width during molecular depth profiling to determine the optimum parameters that lead to the highest information content.

A robust and reproducible model system with well-defined chemical structures is a first step in obtaining quantitative information about buried interfaces using cluster ion bombardment. Previously, we have utilized trehalose sugar films spin-cast on Si substrates to develop an erosion model that uses the damage cross section, the altered layer thickness at the surface and the sputtering yield as parameters.3;16 A different system consisting of organic delta layers built by a large tetrahedral molecule, Irganox, has also been reported.25 Results using this system have shown that the interface width is larger than the delta layer thickness (2.5 nm) and is limited mainly by the development of surface topography. Recently, we also reported on using Langmuir-Blodgett (LB)

82 techniques to form chemically alternating organic thin films as a molecular depth profiling model to study organic-organic interfaces.33 Multilayer LB films have been well-characterized and are known to form sharp boundaries between the layers. The preliminary study showed that chemical structures were accurately represented by the profile of molecule-specific ion signals and that depth resolution can be calculated by a simple curve fitting approach.33 No evidence for topography formation was noted during the erosion process.

Using chemically alternating LB multilayers as a model, here we investigate the experimental parameters necessary for optimization of molecular depth profiling, particularly so that optimum depth resolution can be achieved. The system consists of alternating barium arachidate (AA) and barium dimyristoyl phosphatidate (DMPA) layers

+ ~50 nm thick that is depth profiled by a C60 ion beam. Various parameters that potentially affect the depth profile results are studied, including experimental temperature, sample roughness, primary ion energy and incident angle. Our results show that chemical damage accumulation is minimized when the sample is maintained at liquid nitrogen (LN2) temperature. Samples with slightly different topography yield similar depth resolution, implying that this property is not largely affected by surface roughness.

The parameters of the primary ion beam also have large effects on the profile quality.

For example, the highest depth resolution is achieved at glancing incident angles, but the observed interface widths decrease slightly with increasing kinetic energy. In general, this model system provides a platform for determining the condition for optimum depth resolution and for elucidating fundamental aspects of the interaction of energetic cluster ion beams with molecular solids.

83 5.2 Experimental Section

5.2.1 Materials

Arachidic acid, barium chloride (99.999%), potassium hydrogen carbonate

(99.7%), copper (II) chloride (99.999%) and all solvents were purchased from Sigma-

Aldrich (Allentown, PA). The DMPA was purchased from Avanti Polar Lipids

(Alabaster, AL). All chemicals were used without further purification. Water used in preparation of all LB films was obtained from a Nanopure Diamond Life Science

Ultrapure Water System (Barnstead International, Dubuque, IA) and had a resistivity of at least 18.2 MΩ-cm.

5.2.2 Substrates and film preparation

A 3x3-inch single crystal (100) silicon wafer was used as the substrate for all LB films. The substrates were treated by 3 types of cleaning methods before LB film application. The substrate was either sonicated in methanol for 10 min, or treated with ozone for 10 min, or cleaned by piranha etch (3:1 H2SO4/H2O2). (Extreme caution must be exercised when using piranha etch. An explosion-proof hood should be used.) After cleaning, the substrates were rinsed with high purity water several times to ensure hydrophilicity of the Si/SiO2 surface. A Kibron μTrough S-LB (Helsinki, Finland) was used for isotherm acquisition and multilayer LB film preparation. Details of the LB film formation have been described previously.34 The value of the area/molecule during film transfer is used to calculate the film density needed for sputter yield calculations. At least

84 3 layers of AA were initially applied onto the substrate at first to ensure orderly multilayer formation. Subsequently, an even number of DMPA or AA layers were deposited consecutively. At least 15 min was allowed to elapse between subsequent deposition cycles to ensure complete drying of the substrate.

5.2.3 Instrumentation

A previously described TOF-SIMS instrument was employed for all

35 experiments. Depth profiling of the LB films was performed by a 40-keV C60 ion source (IOG 40-60, Ionoptika; Southampton, U.K.), which is directed to the target surface at an angle of 40º relative to the surface normal. The kinetic energy of the primary ions was adjusted by varying the anode voltage between 20 and 40 kV or by selecting the charge state of the primary ions by means of a Wien filter. The mass spectrometer was operated in a delayed extraction mode with 50 ns delay time between the primary ion pulse and the secondary ion extraction pulse. Charge compensation was found to be unnecessary for the positive ion SIMS mode. Secondary ion intensities were calculated by integrating the respective mass peak in the TOF spectrum. A mass resolution of ~2500 was routinely achieved at the mass of the molecule-specific peak of

DMPA at m/z 525. The incident angle of the projectile ion beam was altered by tilting the sample surface relative to the stage. Although this procedure prevents comparison of ion yields at different angles since the angle between the surface normal and the ion optical axis of the mass spectrometer also changes, ion yields acquired during a depth profile are comparable since the angle is kept constant during the data acquisition.

85 A depth profile was performed by alternating between mass spectral data acquisition and sputter erosion cycles. During an erosion cycle, the films were bombarded with the projectile ion beam operated in dc mode and rastered across a surface area (“field of view”) of dimensions Δx⋅Δy with Δyx=Δ cosθ and Δx ranging from 300 to 600 µm. (The angle θ is the impact angle of the primary beam with respect to the surface normal). A digital raster scheme with 256 x 256 pixels was employed, thus rendering a pixel step size between 1.2 and 2.4 µm, a value that is small compared to the probe size of the projectile beam (∼30 µm). The total bombardment time during each erosion cycle varied from 3 to 10 sec, resulting in a total dwell time between 50 and 150

µs on each pixel. In order to minimize re-deposition effects and ensure a uniform erosion rate, several frame scans were made during each erosion cycle, limiting the pixel dwell time in each individual frame to 10 µs. Between erosion cycles, SIMS spectra were taken from the center of the sputtered region, with the ion beam operated in pulsed mode (pulse duration ∼ 50 ns) and rastered across a quarter of the erosion area. The total projectile ion fluence applied during each acquisition cycle was kept below 1011 cm-2, ensuring negligible erosion even when accumulated over hundreds of data points in the depth profile.

5.2.4 Ellipsometry and AFM measurement

AFM (Nanopics 2100, KLA-Tencor, San Jose, CA) was used to measure the surface roughness and the sputter crater depth. The maximum field of view of 800 µm x

800 µm in contact mode allows a convenient one-step measurement of the entire sputter

86 crater. The thickness of the LB monolayers was determined by a single-wavelength

(632.8 nm, 1 mm spot size, 70° angle of incidence) Stokes ellipsometer (Gaertner

Scientific Corporation, Skokie, IL; model LSE). The thickness of the LB films was found to be equal to the number of layers multiplied by the monolayer thickness.

5.3 Results and Discussions

We have previously demonstrated that LB films represent good model systems for quantitative examination of molecular depth profiling with particular emphasis on the organic-organic interface width.33 The goal in this work is to optimize the depth resolution in such experiments by investigating the role of various experimental parameters with regard to both the operation of the TOF-SIMS instrumentation and to sample preparation. The quality of the depth profile is also determined using parameters evaluated from the previously developed erosion dynamics model.16

5.3.1 Single component LB films

Single component LB films of AA or DMPA are building blocks for alternating

+ LB films and were therefore examined first by C60 depth profiling as a reference for later profiles on multilayer structures. The two single component samples contain 39 layers of

AA or 40 layers of DMPA on top of 3 layers of AA, leading to total film thicknesses of

105 nm (AA) or 96 nm (DMPA), respectively. It is important to note that DMPA multilayers do not form directly on Si but can be built on top of 3 layers of AA that are

87 first deposited on the Si substrate. Since the DMPA layer is much thicker than the bottom AA layers and the signal of AA is not observed in the depth profile, this sample is still considered to be a single component film.

Depth profiling was performed both at room temperature (RT) and at cryogenic temperature with the sample stage continuously cooled by liquid nitrogen (LN2). The resulting profiles are shown in Figure 5-1 . Representative molecular signals of AA and

DMPA at m/z 463 and m/z 525, respectively, are plotted together with a substrate signal

+ + + at m/z 112 for Si4 . The Si4 ion signal is used in place of the Si ion signal since there is less isobaric interference at m/z 112 than at m/z 28. The depth profiles can be divided into three specific regions. At the beginning, the molecular ion signal increases to a maximum and decreases very slightly afterwards. This “surface transient” region looks very similar in all four profiles depicted in Figure 5-1. The characteristics of the second region - where the bulk of the LB film is being continuously removed - vary as a function of the sample temperature. While the LN2 profile exhibits a steady state which persists until the film is completely removed, the RT profile exhibits a gradual decline of the molecular ion signal. The third region is characterized by the interface between the organic layer and the silicon substrate, where the molecular ion signals decrease rapidly and the Si ion signal emerges.

R.T. LN 12000 2 (a) m/z 463 AA 10000 m/z 112 Si

8000

6000

4000

Signal (Counts) Signal 2000

0 50 100 150 200 250 Fluence (x1012ions/cm2)

R.T. LN (b) 12000 2 m/z 525 DMPA 10000 m/z 112 Si

8000

6000

4000 Signal (Counts) 2000

0 50 100 150 200 250 Fluence (x1012ions/cm2)

Figure 5-1: Depth profiles of single component LB films of (a) 105 nm AA, and (b) 96 nm DMPA deposited on piranha etched silicon substrates. Sputter erosion and data + acquisition was performed using 40-keV C60 projectiles. Darker lines denote profiles measured at room temperature (R.T.) and brighter colored lines represent profiles measured at liquid nitrogen (LN2) temperature. Note that m/z 463 was not observed in DMPA spectrum and m/z 525 was observed in AA spectrum.

89 The initial signal increase appears to be mainly associated with the removal of surface contamination. This interpretation is corroborated by the finding that the initial transient is much less pronounced in depth profiles taken of freshly prepared films. The behavior is in contrast to the surface transient associated with peptides in trehalose where a much larger increase in the quasi-molecular ion (M+H)+ is observed. This difference

+ might be associated with the observation that C60 ion bombardment effectively increases the proton concentration in the near surface region. Protonation is presumably not involved in the ionization mechanism for the barium salt studied here, hence resulting in different behavior at low fluence.

The small decay of the molecular ion signal immediately after the initial surface transient is of special interest. This decay has been described quantitatively using a simple erosion dynamics model developed previously.18, 22, 24, 33 With this model the signal is predicted to decrease exponentially to a steady state value due to the building of chemical damage induced by the primary ion beam. In addition, there may be a slower decay of the steady state signal due to a reduction of the total sputtering yield or erosion rate. Although the cause of this reduction is not known at the moment, we speculate that it arises from the formation of small carbon particles that eventually agglomerate. It is

+ known that graphitic carbon has a significantly reduced sputtering yield under C60 bombardment.

From the erosion dynamics model, the steady state signal Sss is related to the initial signal S0 determined by extrapolation to zero fluence as Eq. 5-1

Y tot [Eq. 5- SSSS = 0 tot Ynd+ σ d 1]

90 tot where Y is the total sputter yield, σd is the damage cross section, d the altered layer thickness and n the molecular number density of the film.16 The significance of these parameters has been discussed in detail recently. In particular, the magnitude of the exponential decay is connected to a clean-up efficiency parameter ε, which is determined in Eq. 5-2

Y tot ε = [Eq. 5- ndσ d 2]

As is clear from the data in Figure 5-1, there is virtually no exponential decay in

tot the molecular depth profiles, meaning Y >> ndσd and ε is very large, both at RT and at

LN2 temperature. There is, however, a significant slow decay of the signal for the RT samples. Although the mathematical form of Ytot(f) is not know, a slow exponential

+ 22 decay has been found to fit the data for C60 bombardment of Irganox films at RT.

Since the decay rate is very slow, it can be approximated by a linear relation as shown in

Eq. 5-3

YfYtot( ) = tot (01)⋅−⋅ af [Eq. 5- [ ] 3] where a is a decay cross section related to sputtering. If we assume that the measured molecular ion signal at any given fluence S(f) is proportional to Ytot(f), then

[Eq. 5-

4] and a is easily determined from the depth profile. From the data in Figure, it is clear that

2 the value of a is nearly zero for the LN2 samples. It is ~1 nm for AA at RT and ~0.2

2 + nm for DMPA at RT. For Irganox films bombarded by 30-keV C60 ions at RT, a value

91 2 24 of 0.6 nm is reported (represented as σDS), in reasonable agreement to the findings reported here.

5.3.2 Multilayer structures

The next step is to examine the behavior of alternating multilayer LB films.

Depth profiles acquired at RT and LN2 temperature are shown in Figure 5-2 for a film consisting of 6 building blocks of either AA or DMPA multilayers. Beginning at the surface (top), blocks 1 and 3 each contain 20 layers of DMPA (44 nm), while blocks 2 and 4 consist of 20 layers of AA (54 nm). Blocks 5 and 6 are slightly thicker and consist of 22 layers of DMPA (48 nm) or 23 layers of AA (62 nm), respectively (Figure 5-2a).

In both profiles, the molecular ion signal representing the uppermost DMPA block is found to increase after initial ion bombardment, in the same fashion as seen for the single component films. The apparent AA signal visible at the beginning of the RT profile increases slightly, presumably due to isobaric surface impurities, since the mass spectrum measured in this region is quite different from that measured within an AA block. Upon further irradiation, the two signals continue to alternate in intensity until the Si interface is reached, thus correctly reflecting the chemically alternating structure of the film.

(a) DMPA 44 nm (20 layers)

AA 54 nm (20 layers)

DMPA 44 nm (20 layers)

AA 54 nm (20 layers)

DMPA 48 nm (22 layers)

AA 62 nm (23 layers)

(b) 8000 m/z112 Si 7000 m/z 525 DMPA ÷5 6000 m/z 463 AA 5000 4000 3000 2000

Signal (counts) 1000 0 -1000 -100 0 100 200 300 400 500 600 700 Fluence (x1012ion/cm2)

5000

4000

3000 m/z 463 AA m/z 525 DMPA 2000 m/z 112 Si Signal (Counts) 1000

0 100 200 300 400 500 12 2 Fluence (x10 ions/cm )

Figure 5-2: (a) the chemical structure of the alternating LB film of AA and DMPA deposited on piranha etched silicon substrate and the depth profiles measured at (b) room + temperature and (c) liquid nitrogen temperature using 40-keV C60 projectiles.

93 The most significant difference between the two profiles displayed in Figure 5-2 is the apparent loss of contrast with increasing depth, which is observed in the RT profile but is less pronounced at LN2 temperature. It is tempting to attribute this finding to a degradation of depth resolution with increasing eroded depth, however, this effect would lead to a symmetric decrease and increase of the signal maxima and minima respectively, leaving the average signal largely constant. Instead, the signal maxima observed in

Figure 5-2b decreases about a factor of 2.3 when comparing the beginning block to the final block, while the signal minima remain virtually unchanged. Hence, we conclude that the apparent loss of contrast in the RT data is mainly attributed to a reduction of the

(average) molecular ion signal.

In addition to a decrease in the contrast observed for the RT profile, the erosion rate is observed to decrease with fluence. Assuming the DMPA-AA interface is located at the points where the representative signals match, it is possible to calculate the average sputter yield for each block from the known fluence and block thickness. These yields are reported in Table 5-1 for both the RT and LN2 temperature depth profiles. Note that the total sputter yield drops by ~30% for the RT sample, but is virtually constant for the

LN2 sample. These yields are plotted in Figure 5-3 and are seen to decrease nearly linearly with fluence as predicted by Eq.5-3, using a sputter yield reduction cross section of ~0.14 nm2. Interestingly, this value is smaller than that determined for the single component films. It is, however, similar to that determined for cholesterol films21 under the same bombardment conditions as employed here, indicating that the fluence dependent sputter yield reduction might be a rather general observation in C60 sputter depth profiling.

+ Table 5-1: Sputter Yields (molecule equivalents/C60 ) of DMPA and AA. The data of single component film represent averages of at least 3 parallel experiments of samples with the same chemical structure. Single Alternating film component Middle Bottom film Top block block block Room temperature 329 ± 15 294 248 207 AA Low temperature 448 ± 18 421 408 427 Room temperature 123 ± 7 133 107 94 DMPA Low temperature 166 ± 9 159 164 168

1.0 AA DMPA 0.9 (0)

tot 0.8

(f) / Y tot

Y 0.7

0.6

0 5 10 15 20 25 30 ion fluence (1013 cm-2)

Figure 5-3: Total sputter yield vs. primary ion fluence during depth profiling through alternating LB multilayer film. The data were normalized to the value at the beginning of the depth profile.

It is interesting to note that the molecular ion signal drop observed in Figures 5-1 and Figure 5-2 is larger than that of the total sputter yield. For instance, the DMPA sputter yield drops to 80% and 71% from the top to the middle and bottom block of the multilayer sample, while the signal maxima drop to 50% and 30% respectively. A similar trend is observed for the AA films and the AA blocks. This observation is

95 consistent with the erosion dynamics model, which predicts the “quasi steady state”

δ signal varies as (Y tot ) with values of δ between 1 and 2, depending on whether the clean-up efficiency is large (δ ∼ 1) or small (δ ∼ 2) (see Eq 5-1)

In summary, the RT depth profiles exhibit a drop in yield with fluence that is not observed for the LN2 temperature experiments. It is not clear why the temperature exerts this effect on the profile, but it is not likely related to any change of the film chemistry, since the mass spectra are essentially the same as those obtained at RT. The LN2 depth profiles of LB films exhibit less chemical damage. Hence, subsequent studies are performed exclusively under LN2 conditions.

5.3.3 Surface Topography

The essential step in construction of LB multilayer films is to begin with a well- ordered initial monolayer. A common strategy for preparing the Si substrate is piranha etch which is effective at removing organic adducts and ensuring hydrophilicity. The etching process, however, leads to enhanced surface roughness. Since the roughness of the resulting LB films might be related to the roughness of the starting Si surface, smoother Si substrates are needed to achieve artifact-free measurements of the depth resolution. Two additional methods were developed to explore the importance of topography on the depth profiles. With one scheme, the Si is exposed to UV ozone for

10 min and with a second scheme, the Si substrates are sonicated in methanol for 15 min.

Both procedures were followed by rinsing with ultra pure water to ensure hydrophilicity.

The alternating LB films were then synthesized in the same fashion as described

96 previously. The root-mean-square roughness values measured for Si and the LB films before and during the depth profile analysis are listed in Table 5-2. As expected, the methanol-cleaned substrates yield the smoothest LB films and the piranha-etched films exhibit the most topography. The resulting LB films are usually about 10 nm rougher than their original substrates. However, the roughness does not change significantly after

+ C60 bombardment at LN2 temperature for any of the films studied here.

Table 5-2: Surface Roughness (nm) (roughness average Ra with the field-of-view of 20 µm x 20 µm) of Si substrate and resulting LB films. The data are based on at least 3 parallel measurements. LB film before LB films after Si sputtering sputtering Methanol 1.1 ± 0.2 9.5 ± 1 8.7 ± 1 clean Ozone clean 2.7 ± 0.8 13 ± 2 12 ± 2 Piranha each 4.8 ± 1 16 ± 2 15 ± 2

Representative depth profiles for each of these films are shown in Figure 5-2c and

Figure 5-4 . Qualitatively, the three depth profiles are similar in shape as expected. The fluence value needed to reach the Si interface is also about the same for the three profiles, suggesting that sample topography does not change the sputter yield significantly. The difference in signal intensity is due to the use of a different primary ion current during acquisition of the spectra. The profile of the LB film on methanol-treated substrates

Figure 5-4b has a relatively lower AA signal compared to that of DMPA, although the signal contrast is still about the same as that in other profiles. The post-interface dip in the Si signal observed in the profile of Figure 5-4a probably arises from the formation of a silicon oxide layer formed during O3 treatment of the substrate.

m/z 112 Si 2000 m/z 525 DMPA m/z 463 AA 1500

÷5 1000

500 Signal (Counts) Signal

0 100 200 300 400 12 2 Fluence (x10 ions/cm )

(b) 1500 ÷5

1000

m/z 112 Si 500 m/z 525 DMPA m/z 463 AA Signal (Counts)

0 100 200 300 400 12 2 Fluence (x 10 ions/cm )

Figure 5-4: Depth profiles of alternating LB film of AA and DMPA deposited on silicon substrate cleaned with (a) ozone treatment and (b) methanol sonication measured at liquid + nitrogen temperature using 40-keV C60 projectile ions.

98 It is possible to estimate the depth resolution of alternating multilayer films utilizing the signal contrast in the measured depth profile.33 The “interface width”, i.e., the full half width of the (Gaussian) depth response function, determined in this way is plotted against the depth of the interface for all three profiles depicted in Figure 2c and

Figure 5-4. In all three cases, the interface width is found to increase with increasing depth. A linear fit of the data displayed in Figure 5-5 shows that a rougher sample exhibits a larger increment of the interface width with increasing depth. However, when extrapolated to zero depth, the (virtual) interface width at the beginning of the ion bombardment is ~15 nm in each case. There are many factors that could contribute to the measured interface width. These include i) the depth of origin of the sputtered secondary ions, ii) ion induced interface mixing effects and iii) lateral fluctuations of the LB film thickness. With the latter being of the order of 10 nm – as deduced from the roughness measurements – we estimate 5-10 nm of the zero depth interface width is attributed to the

“intrinsic” depth resolution of the method. This finding is consistent with model computer simulations of 20-keV C60 bombarding Ag, which indicate the formation of an altered layer thickness of several nm.10;11 Moreover, the depth of origin of Ag+ ions ejected through a 2.5 nm ice overlayer is estimated to be about 7 nm at 20-keV.18

34 Piranha 32 Ozone 30 Methanol 28 26 24 22 20 18 Interface Width (nm) Interface 16 14 0 50 100 150 200 Depth (nm)

An interesting question remains regarding the cause of the different slopes observed in Figure 5-5. Apparently, an initially rougher film exhibits a larger degradation of depth resolution with increasing eroded depth. It is tempting to attribute this observation to the development of further, ion bombardment induced roughness at the bottom of the eroded crater. In fact, topography has been suggested to largely determine the observed depth resolution during the analysis of Irganox3114 delta layers embedded in an Irganox1010 matrix25. However, this effect can be excluded here, since the roughness measured after erosion of a significant part of the film is similar to that measured on the original surface. The observed degradation of depth resolution must therefore be induced by an accumulation of ion induced interface mixing during the

100 removal of the film. Why this should depend on the original roughness of either the substrate surface or the deposited film surface is unclear at the present time.

5.3.4 Primary ion energy and incident angle effects

All depth profiling experiments presented so far have been performed with 40-

+ keV C60 ions impinging under an incident angle of 40º relative to the surface normal. In this section, the role of projectile impact energy and angle is studied. Note that all results presented below were obtained on alternating LB films built on ozone-treated substrates analyzed at LN2 temperature.

+ 2+ The depth profiles using 20, and 40-keV C60 and 80-keV C60 ions for both sputter erosion and data acquisition are shown in Figure 5-6 (a), 5-4(a), and 5-6(b), respectively. The ion fluence required to reach the Si interface is ~1x1014 cm-2 at 80-keV,

2x1014cm-2 at 40-keV, and 4x1014 cm-2 at 20-keV. As discussed above, this number is related to the total sputter yield, which is found to increase linearly with projectile impact energy. This observation agrees with results obtained for C60 bombardment of other systems29. Comparing the linear slope of the yield vs. energy curve by means of the

25 3 reduced sputter yield volume Ytot/n,. we find the resulting average value of 3.8 nm removed per C60 ion and keV of impact energy to agree well with values of 4 to 8 nm3/keV measured for trehalose 35, cholesterol21, and Irganox1010 films25.

101

(a) m/z 112 Si 4000 m/z 525 DMPA m/z 462 AA 3000 ÷5 2000

1000 Signal (Counts)

0 100 200 300 400 500 12 2 Fluence (x10 ions/cm ) 4000 m/z 112 Si (b) m/z 525 DMPA 3000 m/z 463 AA ÷5

2000

1000 Signal (Counts)

050100150 12 2 Fluence (x10 ions/cm )

Figure 5-6: Depth profiles of alternating LB film of DMPA and AA deposited on ozone- + treated substrate measured at liquid nitrogen temperature using (a) 20-keV C60 and (b) 2+ 80-keV C60 projectile ions.

In addition to the difference in sputter yield, the 20-keV depth profile appears to be essentially the same as the 40-keV depth profile, while at 80-keV the signal maxima gradually decline with increasing ion fluence. At the same time, the fluence needed to

102 remove the individual layers again increases with increasing depth as was found for the

RT depth profiles noted above. At 80-keV bombardment, then, there is a fluence dependent yield reduction even at LN2 temperature. Apparently, the yield reduction is induced by a thermally activated process which is more likely to occur at higher impact energies.

It is possible that the yield reduction is caused by accumulation of carbon precipitates at the surface of the bombarded film. There is strong experimental36 and theoretical37 evidence that a fraction of incident projectile atoms are being implanted into the irradiated surface. In fact, this effect is known to lead to a complete quenching of the

+ 38;39 sputter yield if Si is bombarded with C60 ions of less than 10-keV. A similar effect has been observed for Irganox films. The notion is that the deposited carbon atoms form precipitates of an amorphous, graphite-like structure 40 which is known to have a very low sputter yield.41;42 Simulations and experiments performed on SiC targets show that single C atoms distributed evenly within a Si crystal do not produce a significant yield reduction.41 In order to be effective, the implanted carbon atoms need to cluster and eventually form precipitates. At low temperatures, the mobility of the implanted projectile atoms is decreased and the formation of carbon precipitates is hindered, thereby efficiently suppressing the yield reduction. At larger impact energy, on the other hand, more energy is deposited in a single impact, increasing mobility and, hence, counterbalancing the effect of reduced temperature.

The interface width as a function of depth and primary ion kinetic energy are shown in

Figure 5-7(a). For all three impact energies, the interface width scales linearly with depth with a slightly different slope. The zero depth interface width as a function of the

103 primary ion energy is shown in Figure 5-7b. Lower impact energy clearly leads to better depth resolution, a finding which is well-known for inorganic systems.43 This effect is understandable since the zero depth interface width depends upon the altered layer thickness which increases with increasing energy. By extrapolating to zero impact energy, a virtual interface width is obtained which should to first order be stripped of bombardment induced effects. In principle, this value should be solely determined by the information depth of the (static) method applied to analyze the surface chemistry. The reported value of about 11.5 nm, however, appears to reflect mainly the fluctuations of film thickness (about 10 nm, see above). More detailed artifact-free measurements of this parameter will be increasingly difficult since it appears to approach a value of just a few nm.

40 80 KeV 22 35 40 KeV 20 KeV 20 30 18 25 16 20 14

Interface Width (nm) 15 12

10 Interface Width at zero depth (nm) 10 0 50 100 150 200 0 20406080100 Primary Ion Energy (KeV) Depth (nm) Figure 5-7: (a) Interface width increment with depth for alternating LB films (ozone treated substrates) for different primary ion energy, and (b) Interface width at zero depth plotted against primary ion energy. The error bars are ±5% of the calculated value.

104 The effect of incident angle on the depth resolution is quite dramatic. The

+ representative depth profiles of the alternating LB films using 40-keV C60 at glancing angle (73º relative to surface normal) and near-normal incidence (5º relative to surface normal) are shown in Figure 5-8 . The comparable profile at 40º incidence is displayed in

Figure 5-4a. Under glancing incidence, the profile looks similar to that at 40º incidence.

However, the depth resolution appears to be slightly improved, since the observed signal maxima reach an observable steady state at the center of each block. On the other hand, the result obtained under normal incidence is catastrophic as shown in Figure 5-8(b). The profile barely resolves the alternating chemical structures except that the DMPA signal drops slightly while the AA signal increases from baseline at the first DMPA-AA interface. This result implies that the depth resolution is even larger than the thickness of the chemical block (44 nm for DMPA and 54 nm for AA). MD simulations have shown that the energy of the primary ion is deposited much deeper under normal incidence conditions than oblique impact angles44. At the same time, the altered layer thickness is experimentally measured to be larger as well.21 Apparently, both effects combine to effectively worsen the achievable depth resolution. At glancing impact angle, on the other hand, the primary ions are more like “peeling” off the surface layer, leaving the molecules underneath better preserved. Compared to 40º incidence, however, the enhancement at glancing angle is not as dramatic as the reduction at normal incidence, a finding which also agrees with computer simulations.44

105

0.005 m/z 112 Si m/z 525 DMPA 0.004 m/z 463 AA

0.003 ÷5

0.002

0.001

0.000 Signal NormalizedSignal to Total

-100 0 100 200 300 400 500 600 700 Fluence (x1012 ions/cm2)

(b) ÷5 1500

1000 m/z 112 Si m/z 525 DMPA 500 m/z 463 AA Signal (Counts)

0 100 200 300 400 500 Fluence (x 1012 ions/cm2)

Figure 5-8: Depth profiles of alternating LB film of DMPA and AA deposited on ozone- + treated Si substrate measured at liquid nitrogen temperature using 40-keV C60 projectiles impinging under (a) 73° and (b) 5° with respect to the surface normal.

5.4 Conclusions

106 Using multilayer LB films as a model for molecular depth profiling, various experimental parameters were investigated for their effects on the quality of depth profiling. The results show that profiles with relatively stable signal maxima and uniform sputter yield are achieved by lowering the sample temperature to cryogenic condition.

The depth resolution is found to deteriorate slightly with increasing primary ion fluence, an effect which does not appear to be directly related to increasing ion induced roughness.

The parameters of the primary ion beam also play an important role in optimizing the molecular depth profiling experiment. The depth resolution is found to be improved at

+ lower C60 kinetic energy, the zero depth interface width scaling linearly with impact energy. If extrapolated to zero impact energy, we find a virtual interface width that is to a large extent determined by fluctuations of the LB film thickness, leaving only a few nm as the physical limit of the achievable depth resolution. Variation of the projectile impact angle reveals that the depth resolution is slightly enhanced under glancing incidence

(compared to 40º impact), while the quality of the depth profile is much worse under normal incidence. These observations agree with the predictions of MD computer simulations. In summary, we suggest use of the lowest possible impact energy – which is compatible with good beam focusing conditions needed for high resolution three- dimensional imaging applications – and glancing incidence in combination with low sample temperature to achieve optimum depth resolution in molecular depth profiling experiments.

107 5.5 Acknowledgement

Financial support from the National Institute of Health under grant # EB002016-

13, the National Science Foundation under grant # CHE-555314, and the Department of

Energy grant # DE-FG02-06ER15803 are acknowledged. The authors also thank Prof.

David L. Allara and his research group for the use of ellipsometry equipment, and

Dr.Joseph J. Kozole for building the special sample holder for incident angle experiments.

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20. Gillen, G.; Batteas, J.; Michaels, C. A.; Chi, P.; Small, J.; Windsor, E.; Fahey, A.;

Verkouteren, J.; Kim, K. J. Appl.Surf.Sci. 2006, 252, 6521-25.

21. Kozole, J., Wucher, A., and Winograd, N. Anal.Chem. in press, 2008.

22. Mahoney, C. M.; Fahey, A. J.; Gillen, G. Anal.Chem. 2007, 79, 828-36.

23. Mahoney, C. M.; Fahey, A. J.; Gillen, G.; Xu, C.; Batteas, J. D. Anal.Chem. 2007,

79, 837-45.

24. Shard, A. G., Green, F. M., Brewer, P. J., Seah, M. P., and Gilmore, I. S.

J.Phys.Chem.B 2008, 112, 2596-2605.

109 25. Shard, A. G.; Brewer, P. J.; Green, F. M.; Gilmore, I. S. Surf.Interface Anal. 2007,

39, 294-98.

26. Wagner, M. S. Anal.Chem. 2004, 76, 1264-72.

27. Delcorte, A.; Garrison, B. J. Journal of Physical Chemistry C 2007, 111, 15312-24.

28. Postawa, Z.; Czerwinski, B.; Winograd, N.; Garrison, B. J. J.Phys.Chem.B 2005,

109, 11973-79.

29. Russo, M. F.; Szakal, C.; Kozole, J.; Winograd, N.; Garrison, B. J. Anal.Chem.

2007, 79, 4493-98.

30. Smiley, E. J.; Winograd, N.; Garrison, B. J. Anal.Chem. 2007, 79, 494-99.

31. Fletcher, J. S.; Lockyer, N. P.; Vaidyanathan, S.; Vickerman, J. C. Anal.Chem. 2007,

79, 2199-206.

32. Jones, E. A.; Lockyer, N. P.; Vickerman, J. C. Anal.Chem. 2008, 80, 2125-32.

33. Zheng, L.; Wucher, A. W. N. J.Am.Soc.Mass Spectrom. 2007.

34. Braun, R. M.; Blenkinsopp, P.; Mullock, S. J.; Corlett, C.; Willey, K. F.; Vickerman,

J. C.; Winograd, N. Rapid Commun.Mass Spectrom. 1998, 12, 1246-52.

35. Wucher, A., Cheng, J., and Winograd, N. Appl.Surf.Sci. in press, 2008.

36. Gillen, G.; Batteas, J.; Michaels, C. A.; Chi, P.; Small, J.; Windsor, E.; Fahey, A.;

Verkouteren, J.; Kim, K. J. Appl.Surf.Sci. 2006, 252, 6521-25.

37. Krantzman, K. D., Kingsbury, D. B., and Garrison, B. J. Appl.Surf.Sci. 2006, 252,

6463-6465.

38. Gillen, G.; Batteas, J.; Michaels, C. A.; Chi, P.; Small, J.; Windsor, E.; Fahey, A.;

Verkouteren, J.; Kim, K. J. Appl.Surf.Sci. 2006, 252, 6521-25.

110 39. G. Fisher, data presented at the IUVSTA workshop on cluster surface interaction,

Barony Castle, Scotland, April 2007.

40. Gillen, G.; Batteas, J.; Michaels, C. A.; Chi, P.; Small, J.; Windsor, E.; Fahey, A.;

Verkouteren, J.; Kim, K. J. Appl.Surf.Sci. 2006, 252, 6521-25.

41. Krantzman, K. D., Webb, R., and Garrison, B. J. Simulations of C60 bombardment

of Si, SiC, diamond and graphite. Appl.Surf.Sci. in press, 2008.

42. J. Kozole, A. Wucher and N. Winograd, unpublished data

43. Hofmann, S. Sputter-depth profiling for thin-film analysis. Philos.Tr.R.Soc.S-A

2004, 362, 55-75.

44. Ryan, K. E.; Garrison, B. J. Appl.Surf.Sci. 2007.

Chapter 6

Three-dimensional Imaging of Alternating Langmuir-Blodgett Films for Retrospective Analysis

6.1 Introduction

The use of cluster ion projectiles in secondary ion mass spectrometry has opened new opportunities for organic and biological material characterization.1;2 Molecular depth profiling has become possible with successful applications in various systems.3-8

At this point, a more quantitative understanding of the sputtering process is needed to support further development and application of molecular depth profiling. The number of studies associated with elucidating these issues is growing rapidly. Cheng et al. developed an erosion dynamics model to describe the change of secondary ion intensities with fluence for spin-cast trehalose films.9 The model is based on the balance between the number of sputtered and damaged molecules per projectile impact. Shard and coworkers studied an organic system that contains delta layers and obtained quantitative information regarding sputtering yield, secondary ion intensity, and depth resolution.10

We have also developed Langmuir-Blodgett films as models to quantitatively investigate organic- organic interface widths.11 Most of these studies have focused on the phenomenological parameters of the depth profiling. However, some technical issues are also critical to achieving a successful molecular depth profile, which have not been thoroughly explored.

112 Recently, the concept of three-dimensional imaging has emerged as a result of the combination of molecular depth profiling and chemical imaging. Three-dimensional imaging has been practically applied to tissue and cell analysis.7;12 Besides its application to real systems, three-dimensional imaging is also useful for molecular depth profiling if the sample system has known chemical structures. Previously, we have shown that Langmuir-Blodgett (LB) films are good model systems for the study of molecular depth profiling investigations. In this study, alternating LB films were used as

+ a three-dimensional imaging target and analyzed by a 40-keV C60 ion beam. The comparison of the reconstructed three-dimensional image and its original structure provides a clear evaluation of the sputtering process. Furthermore, the erosion rate is not uniform across the evolving sputter crater. This effect was quantitatively studied by comparing depth profiles extracted from different positions within the eroded crater and from varying data acquisition area around the center of the crater. The results provide a path to estimating the artifact-free depth resolution of this approach.

6.2 Experimental Section

6.2.1 Materials and film preparation

The following materials were used without further purification: AA, barium chloride, potassium hydrogen carbonate, and copper (II) chloride (all purchased in powder from Sigma-Aldrich Co., St.Louis, MO), DMPA (Avanti Polar Lipids, Inc.,

Alabaster, AL), methanol, and chloroform. The water used was purified by a Nanopure

113 Diamond Life Science Ultrapure Water System (Barnstead International Inc. Dubuque,

IA).

LB film preparation and characterization have been described in detail in the experimental section of Chapter 4 and Chapter 5. The film alternates between barium arachidate (AA) and barium dimyristoyl phosphatidate (DMPA) with their specific SIMS peaks at m/z 463 and m/z 525.

6.2.2 Three dimensional imaging and data processing

The three-dimensional imaging experiments were performed by the TOF-SIMS instrument described in Chapter 1. The C60 ion source was operated at 40-keV with an angle of 40 degree relative to the surface normal. The three-dimensional imaging experiments are carried out in the same way as conventional depth profiling by alternating between sputter erosion and data acquisition cycles. During data acquisition,

SIMS images are collected at 20 shots/pixel with 128 x 128 pixels covering a 400 µm2 raster area. All detected secondary ions were save so that the three-dimensional distribution of any desired mass can be extracted in retrospect from the acquired data set.

Sputter erosion of the film was performed with the ion beam switched to direct current

(dc) operation and rastered in two different scanning modes. First, an analog raster mode was used where the ion beam is deflected at video rates by internal voltage ramps generated in the ion source raster controller. This mode will in the following discussion be referred to as “analog raster”. Alternatively, the beam was stepped from pixel to pixel in the same way as during image acquisition. In this mode, which will in the following

114 be referred to as “digital raster”, a sputter erosion cycle of predefined length was divided into a number of fast raster scans in order to limit the dwell time on each pixel to about

10 µs per scan. This was done in order to minimize re-deposition of sputtered material during the erosion process, which constitutes a well known problem in focused ion beam technology.

To construct a three-dimensional representation of the sample composition from the acquired image stack, the data were analyzed as follows. First, a range of pixels was masked in the total ion image (i.e., the image summed over all data acquisition cycles of the depth profile), in order to select the lateral area of which a depth profile was to be constructed. Then, a mass range was selected in the total mass spectrum (i.e., the mass spectrum of all detected ions summed over all pixels of all images), and the measured signal was integrated over the selected mass range and stored as a three dimensional array

S(i,j,k) for each pixel (j,k) and image number (i). These “matrix” files were then processed by a Matlab® script to generate input files for the visualization software

Amira®, which was then used to generate a 3D-representation of the selected mass signal.

6.3 Results and Discussion

Sputter depth profile analysis is often influenced by a so-called “crater effect”, where a laterally inhomogenous erosion rate leads to the development of surface topography at the bottom of the eroded sputter crater. Naturally, any erosion-induced topography acts to deteriorate the depth resolution attainable in the analysis. A general strategy to minimize such effects is to restrict the lateral area used for data acquisition as

115 much as possible to the center of the eroded crater. This, however, inevitably leads to a compromise between depth resolution and sensitivity, and the gated area must therefore be carefully chosen. In conventional sputter depth profiling, it is necessary to pre-select the gating area prior to data acquisition, and the only way to judge the suitability of this choice is to acquire multiple depth profiles with different selections. This is where imaging depth profile analysis as performed here becomes extremely useful, since here it is possible to investigate the influence of the gating area by a retrospective analysis of one data set acquired in one single depth profile. This unique feature will be applied in the following subsections to investigate the crater effect in some detail.

6.3.1 Influence of raster mode

In analog raster mode, the eroding ion beam is swept across the analysis field-of- view by means of sawtooth-shaped deflection voltage ramps. As a result of this scanning method, the primary ion beam ends up spending more time at the edge than at the center of the crater, which leads to laterally inhomogeneous erosion. As a common strategy employed in our lab during “conventional” depth profile analysis, SIMS spectra are acquired from a quarter sputtered area and less than half of the sputter eroded area in order to avoid the crater effect. However, there has been no direct evaluation of the remaining crater effect and to what extent it affects the depth.

Using the three-dimensional imaging data set acquired here, it is possible to visibly evaluate the crater effect by retrospective analysis of the multilayer system investigated here. As a first step, the raster mode during sputter erosion is varied

116 between analog and digital as explained in the experimental section. The resulting three- dimensional representations of three mass signals representing DMPA, AA and the Si substrate are shown in Figure 6-1. The image was constructed by overlapping the three signals of DMPA, AA, and Si, in green, red, and blue. Both images clearly represent the original chemical structure of the multilayer sample. However, the layers of AA and

DMPA are displayed as flat and parallel in Figure 6-1(b), where erosion was performed in digital raster mode, while this is clearly not the case in the image acquired in analog mode (Figure 6-1(c)). In the latter case, the layers appear to be curved, the effect becoming worse with increasing depth. These artifacts are caused by the fact that erosion proceeds faster at the edges than at the center of the sputter crater, leading to a difference in crater depths which accumulates with increasing depth. It is clear from Figure 1(c) that this crater effect is still effective even if the analysis field of view is selected much smaller than the sputter crater area, especially at larger depths. Thus the apparent depth resolution determined from data acquired from a quarter of the eroded field of view must still be affected by crater effect. Using a digital raster scheme, this effect is apparently diminished, thus rendering this mode more suitable for depth profiling experiments.

117

(a) DMPA (40 nm)

AA (54 nm)

DMPA (40 nm)

AA (54 nm)

DMPA (44 nm)

AA (62 nm)

(b) (c)

Figure 6-1: (a) Schematic drawing of the alternating LB film for three-dimensional imaging experiment, (b) three-dimensional representation of the alternating LB film reconstructed from TOF-SIMS data with external sputtering, (c) three-dimensional representation of the alternating LB film reconstructed from TOF-SIMS data with TV sputtering. For (b) and (c), the DMPA signal is depicted in green, the AA signal in red, and Si substrate signal in blue.

118 6.3.2 The effect of data acquisition range and position on interface width

In order to further investigate how both the size and position of the data acquisition (“gating”) area affect the result of interface width determination, depth profiles extracted from different subsections of the three-dimensional images are compared in Figure 6-2 . Specifically, depth profiles extracted from an area of 100 x 100

µm2 located at the center and the four corners of the sputter crater as indicated in Figure

6-2(a) are shown. Although the effect of inhomogeneous erosion is not obvious in Figure

6-1(b), it is obvious that the quality of the depth profile greatly depends on the location within the sputter crater even in this case. As expected, the depth profile taken at the center of the crater (Figure 6-2(b)) exhibits highest signal contrast for both AA and

DMPA, thus indicating the highest depth resolution (smallest apparent interface width) to be achieved under these conditions. In contrast, the profile extracted from the upper-right corner looks worst with both smaller signal levels and lower contrast. The profiles in the upper-left and lower-right corners appear intermediate, while the profile taken at the lower left corner exhibits comparable signal contrast as the center profile and even higher signal for the top two chemical layers.

119

100 µm (a) (b) 1000 c d Si 800 AA

400 µm DMPA 600

b 400

200 Signal (Counts) Signal

e f 0

0 100 200 300 400 500 12 2 (c) 1000 (d) 1000 Fluence (x10 ions/cm )

Si Si 800 AA 800 AA DMPA DMPA 600 600

400 400

200 200 Signal (Counts) Signal (Counts) Signal

0 0

0 100 200 300 400 500 0 100 200 300 400 500 Fluence ( x 1012 ions/cm2) Fluence ( x 1012 ions/cm2) (e) 1000 (f) 1000 Si Si 800 AA 800 AA DMPA DMPA 600 600

400 400

200 200 Signal (Counts) Signal (Counts) Singal

0 0

0 100 200 300 400 500 0 100 200 300 400 500 Fluence ( x 1012 ions/cm2) Fluence ( x 1012 ions/cm2) Figure 6-2: (a) Schematic drawing to show the location of corresponding depth profiles displayed in (b) to (f) in the original three-dimensional image. The DMPA signal is depicted in green, the AA signal in red, and Si substrate signal in blue.

120 Since the sample is laterally homogenous and the data acquisition is the same in all cases, the reason behind the different performance of these depth profiles is clearly related to a lateral inhomogeneity of the sputter erosion process. To quantitatively investigate this crater effect further, we examine depth profiles extracted from the center of the crater with different size of the analyzed area. As an example, data extracted from

400 µm, 300 µm, 200 µm, and 100 µm field-of-view are displayed in Figure 6-3. The interface widths in each depth profile are calculated using the contrast-depth resolution relationship developed in Chapter 4. The resulting apparent width of each interface in the multilayer stack is determined and plotted against the depth of the interface in Figure 6-

4(a). It is seen that in all cases the apparent interface width increases linearly with eroded depth, as would be expected from a lateral inhomogeneity of the erosion rate. This finding agrees with the results presented earlier (Chapter 5). Moreover, the apparent width of each individual interface is found to increase with increasing analysis field of view as displayed in Figure 6-4(b).

121

(a) FOV 400 µm (b) FOV 300 µm 8000 5000

6000 4000

Si 3000 4000 Si AA AA DMPA 2000 2000 DMPA 1000 Signal (Counts) Signal (Counts)

0 0

0 100 200 300 400 500 0 100 200 300 400 500 Fluence (x1012 ions/cm2) Fluence (x1012 ions/cm2) (c) FOV 200 µm (d) FOV 100 µm 2500 600 2000 Si Si 1500 AA 400 AA DMPA DMPA 1000 200

500 Signal (Counts) Signal (Counts)

0 0

0 100 200 300 400 500 0 100 200 300 400 500 Fluence (x1012 ions/cm2) Fluence (x1012 ions/cm2)

Figure 6-3: Depth profiles with different field-of-view (FOV) extracted from external- sputtered three-dimensional image (figure 1(b)). The DMPA signal is depicted in green, the AA signal in red, and Si substrate signal in blue.

122

(a) FOV 400 μm 40 FOV 300 μm 35 FOV 200 μm FOV 100 μm 30

20 Interface Width (nm) 15

10 0 50 100 150 200 Depth (nm)

(b) 4th interface 40 3rd interface 2nd interface 35 1st interface at zero depth 30

Interface Width (nm) Interface Width 15

10 0 100 200 300 400 Field-of-View (nm)

Figure 6-4: (a) Interface width from depth profiles extracted from different field-of-view (FOV) are plotted against depth, (b) Interface width

In principle, it should be possible to eliminate the effect of a laterally inhomogeneous erosion rate by extrapolating the measured interface width to zero depth.

The plot displayed in Figure 6-4(a) clearly shows that these extrapolated virtual interface widths depend on the analysis field of view. This finding indicates that other factors

123 besides inhomogeneous sputter erosion must also influence the apparent depth resolution.

Since these cannot be induced by the depth profiling process, they must relate to properties of the original sample itself. In particular, the data displayed in Figure 4(b) indicate fluctuations of the LB film thickness which occur on lateral length scales of hundreds of micrometers. In principle, the influence of such inhomogeneities can be eliminated by extrapolation to zero acquisition area. It is seen that the resulting (virtual) zero area (“point”) interface widths again depend on the depth of the particular interface.

Extrapolating the zero depth values to zero area should in principle completely eliminate the influence of large-scale lateral inhomogeneities. From Figure 6-4(b), the resulting virtual interface width is determined as Δz0 = 13 nm. AFM measurements of the LB surface topography reveal an rms microroughness of the deposited LB film stack which is about 10 nm larger than that of the original Si substrate. The lateral wavelength of this roughness is of the order of sub-µm and therefore not tractable by extrapolation of the sub-mm acquisition area dependence depicted in Figure 6-4(b). We therefore conclude that a significant portion of Δz0 must be attributed to short-scale fluctuations of the original LB film thickness, leaving only a few nm as the “intrinsic” depth resolution of the method. Factors that could contribute to this property include: i) the depth of origin of the sputtered secondary ions and ii) ion induced interface mixing effects. The data reported in Figure 6-4 are consistent with model computer simulations of 20-keV

C60 bombarding Ag, which indicate the formation of a mixing layer thickness of several nm thickness.13 Moreover, the depth of origin of Ag+ secondary ions ejected through a

2.5 nm ice overlayer is estimated to be about 7 nm at 20-keV.14

124 6.4 Conclusions

The three-dimensional analysis of chemically alternating LB multilayer films provides a suitable platform to investigate different effects contributing to the apparent depth resolution in molecular depth profiling experiments. Comparing depth profiles extracted from different lateral regions of the analyzed area centered around different positions within the sputter crater reveal the role played by lateral inhomogeneities of both the erosion rate (“crater effects”) and the sample itself. In this context, the multilayer sample structure is extremely useful, since it allows investigation of the depth dependent degradation of the apparent depth resolution.

It is found that measured interface widths decrease linearly with decreasing analysis area, thus allowing data extrapolation towards zero analyzed surface area. The

“spot” interface width determined this way are found to increase with increasing eroded depth again in a linear fashion which allows to extrapolate to zero eroded depth. The resulting width of about 13 nm characterizes the apparent depth resolution as the half width of the depth response function which is stripped of broadening effects induced by large-scale lateral inhomogeneities of both the sample and the erosion rate. It does, however, still contain a contribution caused by microscopic fluctuations of the sample film thickness, since these cannot be eliminated by the extrapolation procedure. AFM surface roughness measurements suggest the latter to be of the order of 10 nm, thus leaving only a few nanometers as the “intrinsic” depth resolution of the cluster SIMS method employed for mass spectral data acquisition. This finding appears to be in good agreement with molecular dynamics computer simulations as well as other experiments

125 investigating the depth of origin of secondary ions sputtered under conditions similar to those applied here.

6.5 Acknowledgement

The author would like to thank Prof. Andreas Wucher for insightful discussion and manuscript revision.

6.6 References

1. Gillen, G.; Roberson, S. Rapid Commun.Mass Spectrom. 1998, 12, 1303-12.

2. Winograd, N. Anal.Chem. 2005, 77, 142A-9A.

3. Mahoney, C. M.; Roberson, S. V.; Gillen, G. Anal.Chem. 2004, 76, 3199-207.

4. Sostarecz, A. G.; Mcquaw, C. M.; Wucher, A.; Winograd, N. Anal.Chem. 2004, 76,

6651-58.

5. Sun, S.; Szakal, C.; Roll, T.; Mazarov, P.; Wucher, A.; Winograd, N. Surf.Interface

Anal. 2004, 36, 1367-72.

6. Cheng, J.; Winograd, N. Anal.Chem. 2005, 77, 3651-59.

7. Fletcher, J. S.; Lockyer, N. P.; Vaidyanathan, S.; Vickerman, J. C. Anal.Chem. 2007,

79, 2199-206.

8. Jones, E. A.; Lockyer, N. P.; Vickerman, J. C. Anal.Chem. 2008, 80, 2125-32.

9. Cheng, J.; Wucher, A.; Winograd, N. J.Phys.Chem.B 2006, 110, 8329-36.

10. Shard, A. G.; Green, F. M.; Brewer, P. J.; Seah, M. P.; Gilmore, I. S.

J.Phys.Chem.B 2008, 112, 2596-605.

11. Zheng, L.; Wucher, A. W. N. J.Am.Soc.Mass Spectrom. 2007.

126 12. Gillen, G.; Fahey, A.; Wagner, M.; Mahoney, C. Appl.Surf.Sci. 2006, 252, 6537-41.

13. Postawa, Z.; Czerwinski, B.; Szewczyk, M.; Smiley, E. J.; Winograd, N.; Garrison,

B. J. J.Phys.Chem.B 2004, 108, 7831-38.

14. Szakal, C.; Kozole, J.; Russo, M. F.; Garrison, B. J.; Winograd, N. Phys.Rev.Lett.

2006, 96.

Chapter 7

Conclusions and Future Direction

The latest developments in instrumentation and methodology have opened new opportunities for TOF-SIMS as a unique technique in bioanalysis, particularly chemical imaging and depth profiling. This thesis is focused on using LB films as a model biological system for TOF-SIMS analysis. The model system provides a platform for both the fundamental understanding of mechanisms and further development of new applications for TOF-SIMS bioanalysis.

Chemical imaging of cellular membranes by TOF-SIMS has been shown to be useful in the identification and localization of lipids in cellular membranes. Furthermore, specific molecular interactions can be studied by TOF-SIMS imaging of LB monolayer films of lipids, as reported in Chapter 2. Cholesterol is mixed with SM and PC with varying tailgroup saturation levels. The domain formation and localization of cholesterol,

SM, and PC in the monolayer films indicate that the interaction between cholesterol and

SM is dominated by the tailgroup saturation of SM, rather than hydrogen bonding between the two molecules. The result has opened a new application scope of TOF-

SIMS imaging. Molecular interactions between specific lipid molecules can be studied in the same fashion as discussed in Chapter 2, which is otherwise difficult to elucidate in the complex cellular membrane.

Membrane proteins play important roles in cellular membrane functioning. Thus incorporation of membrane proteins is a critical step towards building more biologically

128 relevant model membrane systems. In Chapter 3, LB monolayer films composed of lipid molecules and a membrane protein glycophorin A are imaged by TOF-SIMS. The lipid combination of cholesterol/DPPC and cholesterol/DPPE mimic the outer and inner leaflets of the plasma membrane, respectively. Domain structures are observed for the cholesterol/DPPE/glycophorin A film while the cholesterol/DPPC/glycophorin A film forms a homogeneous phase. The imaging results are supported by matrix-effect analysis.

This preliminary approach proves that TOF-SIMS is capable of detecting and identifying membrane proteins in the model system.

In the future, LB model systems containing other membrane proteins can be built with lipid molecules of interest and then can be imaged by TOF-SIMS to better understand their functions in cellular membranes. The candidates include glycosyl- phosphatidyl-inositol (GPI)-anchored proteins and amyloid beta (Aß) peptides. The GPI- anchored proteins reside exclusively outside the membrane and their lipid part only interacts with the outer leaflet, which make them fit into the monolayer membrane better than transmembrane proteins. There has been a great deal of evidence showing GPI- anchored protein as an important part of the raft domains.1-3 The Aß peptides are cleaved from amyloid beta precursor protein in the plasma membrane and they aggregate to form plaques, which is a critical step in the development of Alzheimer’s disease.4 The relatively small size of Aß peptides makes them fit the monolayer system quite well. The molecular weight also falls in the range of detectable mass range of TOF-SIMS. Some evidence have pointed to rafts domain and cholesterol playing a critical role in Aß plaque formation.4-6

129 Besides utilizing LB monolayer films as a model cellular membrane system for

TOF-SIMS imaging, we can also build LB multilayer films as a model system for fundamental studies of molecular depth profiling since they have well-characterized structures and sharp chemical interfaces between the layers. Chemically alternating LB multilayer films of AA and DMPA are introduced in Chapter 4 as a platform for investigations of organic-organic interfaces in molecular depth profiling, together with an interface quantification method. In Chapter 5, this model is used to further examine the effects of different experimental parameters on depth resolution. The results indicate that optimal depth resolution could be achieved by lowering the experimental temperature, using primary ion beams at a lower kinetic energy and a glancing incident angle.

The combination of molecular depth profiling and TOF-SIMS chemical imaging leads to a novel concept of three dimensional imaging, which involves taking images of the sample in a layer-by-layer fashion and reconstructing the original chemical structure.

Although three dimensional imaging has been applied to tissue and cell analysis, there are still many fundamental aspects remaining to be understood. Multilayer LB film systems are a suitable platform for such investigations. In Chapter 6, the crater effect is quantitatively studied by three dimensionally imaging alternating LB multilayer films and the results show that interface widths decrease linearly with decreasing analysis area.

Future developments involve building LB films with three dimensional pattering as a target for three dimensional imaging. The use of model systems with well organized three dimensional structures will enhance the understanding of the imaging process and help developing advanced data analysis procedures.

130 References

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2. Jacobson, K. and Deitrich, C. Trends in Cell Biology 1999, 9, 87-91.

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4. Wood, W.G.; Echert, G.P.; Igbavboa, U.; and Müller, W.E. Biochimica et Biophysica

Acta 2003, 1610, 281-290.

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Nature Medicine 1998, 4, 730-734.

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Murakami, T.; Matsubara, E.; Abe, K.; Ashe, K.H.; and Younkin, S.G. The Journal of

Neuroscience 2004, 24, 3801-3809.

VITA

Leiliang Zheng

Leiliang Zheng was born in Shanghai, China on February 8th, 1979 to Shixian

Zheng and Yinhui Jiao. She attended Fudan University in Shanghai in 1997 and received a Bachelor of Science in Chemistry in 2001. In August of 2001, she began her graduate study in Chemistry at the University of Texas at Dallas. She transferred to the

Pennsylvania State University to continue her graduate study in Chemistry in August

2003 where she joined the research group of Professor Nicholas Winograd. She conducted her research in the area of analytical chemistry and received her Doctor of

Philosophy in 2008.